Trends towards multidrug-resistant bacteria: heterocyclic compounds containing antimicrobial agents: review

Abstract

The rapid emergence of multidrug-resistant (MDR) pathogens poses a severe global health threat, as current antibiotics become increasingly ineffective due to antimicrobial resistance (AMR), irrational drug use across human, veterinary, and agricultural sectors, and aggressive pharmaceutical marketing. This crisis is further aggravated by a shortage of novel antibacterial agents entering clinical practice, highlighting the urgent need for new treatment modalities and drug repurposing strategies. In response, heterocyclic compounds have emerged as a highly versatile and promising class of organic molecules with unique broad-spectrum antibacterial activity against both Gram-positive and Gram-negative strains. To successfully translate these bench discoveries into clinical solutions against superbugs, a combined approach integrating rigorous antibiotic stewardship principles with streamlined regulatory pathways is essential.

Rising multidrug-resistant superbugs demand new defenses like heterocyclic compounds, whose clinical success relies on strict stewardship and streamlined regulation.

1. Introduction

The rise of multidrug-resistant (MDR) microorganisms defined as pathogens displaying resistance to at least three distinct antibiotic classes, including that targeting cell wall synthesis, protein synthesis, and DNA replication presents a critical global health threat.¹ Methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus species (VRE), carbapenem-resistant Acinetobacter baumannii and Pseudomonas aeruginosa, and extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales are notable examples.¹ To direct research and development toward novel therapies, the World Health Organization established a priority list evaluating pathogens on mortality, transmissibility, and treatment availability.^2,3 Pathogens are divided into three categories: high priority (vancomycin-resistant E. faecium, carbapenem-resistant P. aeruginosa, MRSA, and fluoroquinolone-resistant Salmonella and Shigella species), medium priority (macrolide-resistant S. pneumoniae and ampicillin-resistant H. influenzae), and critical priority (carbapenem-resistant Enterobacterales, third-generation cephalosporin-resistant Enterobacterales, and carbapenem-resistant A. baumannii).⁴ Driven by selective pressure from inappropriate clinical prescribing, agricultural overuse, environmental contamination, and weak regulatory frameworks, resistance spreads rapidly through spontaneous genetic mutations and horizontal gene transfer (HGT) across human, animal, and environmental domains.^6–8 If left unchecked, antimicrobial resistance (AMR) is projected to cause up to 10 million deaths annually by 2050, alongside cumulative economic losses exceeding USD 100 trillion.^5,6,13–16 Mechanistically, pathogens resist treatment via enzymatic inactivation such as ESBL and carbapenemase production in E. coli and K. pneumoniae that degrade beta-lactam antibiotics⁹ or target site alterations, such as DNA gyrase mutations conferring fluoroquinolone resistance in Salmonella and Pseudomonas species.¹¹ Addressing these clinical challenges—whether from community-associated infections (>48 hours of hospitalization) or nosocomial origin (>48 hours)¹⁹ requires rapid molecular diagnostics like PCR and next-generation sequencing (NGS) to detect resistance mutations.¹² On the therapeutic front, emerging solutions involve novel β-lactamase inhibitor combinations (e.g. ceftazidime-avibactam, meropenem-vaborbactam),¹⁰ drug repurposing, molecular hybridization, and structural optimization of existing compounds.^17,18 Additionally, incorporating innovative chemical approaches, such as microwave-assisted synthetic techniques, is actively accelerating the discovery and development of novel antimicrobial leads to combat the growing antimicrobial resistance (AMR) burden.^20,21

2. Categories of antibiotics and where they ACT on bacteria

The bacterial cell wall and membranes, ribosomes, nucleic acids, bacterial cellular metabolism, and bacterial cellular enzymes are among the targets of the many antibiotics and antibacterial medications. These medicines prevent bacterial growth, multiplication, and destruction by a variety of ways. These consist of (1) beta lactam inhibition of cell wall production, (2) disruption of cell-membrane function, (3) protein synthesis inhibition (50S and 30S) (4) preventing the production of nucleic acids, including DNA and RNA, and (5) acting as antimetabolites (Fig. 1).^22–24

Fig. 1. Classes of antibiotics/antibacterial agents and their modes of action on bacteria.

3. Antibiotic resistance mechanisms in Gram-positive bacteria

A major challenge in the current clinical landscape is the rising incidence of multidrug-resistant (MDR) bacteria, coupled with the limited availability of newly developed antibiotics capable of effectively treating these infections. Consequently, current research efforts are increasingly focused on identifying novel strategies to manage MDR pathogens. In this regard, the World Health Organization has made a significant contribution by publishing a priority list of highly resistant bacterial pathogens that represent a serious global health threat. The WHO has also urged countries worldwide to accelerate the development of new antimicrobial agents and alternative therapeutic approaches to combat MDR infections effectively. This priority list includes several clinically important Gram-positive pathogens, such as methicillin-resistant Staphylococcus aureus, drug-resistant Streptococcus pneumoniae, and vancomycin-resistant Enterococcus faecium, among others, all of which pose a substantial risk to public health due to their increasing resistance to available treatments.²⁵ It has been noticed that such resistance develops in bacteria due to genetic mutations and/or acquired genomes.²⁶ Gram-positive bacteria acquire antibiotic resistance through two primary methods.

These are as follows:

(i) The release of β-lactamases, which break down antibiotics enzymatically.

(ii) By obtaining exogenous DNA or by mutating native PBP genes, which lowers the affinity and sensitivity of their target site, such as PBP (penicillin-binding protein).^27,28

4. Antibiotic resistance mechanisms in Gram-negative bacteria

Since ancient times, natural products have been utilized to treat a wide range of illnesses. For instance, quinine, which is used to treat malaria, is found in the cinchona tree. Numerous antibacterial medications have been created since fleming discovered penicillin in 1929, and they have all significantly impacted human health and mortality rates worldwide.²⁹ New resistant types of antibiotics have emerged as a result of overuse and abuse. Public knowledge of the problem is crucial since people in developing countries can easily access antibiotics without a prescription.³⁰ Through a variety of strategies, such as enzymatic drug inactivation, active antibiotic efflux from the cell, and structural changes to cellular components that lessen drug binding or entrance, bacteria can avoid the effects of antibiotics. Collectively, these strategies contribute to the development and persistence of antibiotic resistance. In general, bacterial resistance is classified into two main types: intrinsic resistance, which is naturally present due to inherent structural or functional characteristics of the organism, and acquired resistance, which arises through the acquisition of resistance genes or genetic material from other bacteria via horizontal gene transfer. The differentiation between Gram-positive and Gram-negative bacteria is based on the Gram staining technique, originally developed by Christian Gram. This method involves the application of a primary stain (crystal violet), followed by iodine as a mordant, and subsequent decolorization and counterstaining with safranin. Gram-negative bacteria lose this complex during decolorization and appear pink because of the counterstain, while Gram-positive bacteria maintain the crystal violet–iodine complex and appear purple. This difference in staining behavior is primarily attributed to variations in cell wall structure and composition between the two bacterial groups.^29,30 The cell envelope of Gram-negative bacteria is composed of three main layers. The outermost layer is the outer membrane, which functions as a protective barrier and distinguishes Gram-negative bacteria from Gram-positive organisms. This membrane exhibits an asymmetric structure, where lipopolysaccharides (LPS) are located in the outer leaflet, while phospholipids are present in the inner leaflet. In addition, the outer membrane contains various proteins, including porins, which facilitate the selective transport of molecules across the membrane. Beneath the outer membrane lies the peptidoglycan layer, which forms the bacterial cell wall. This structure is composed of repeating units of N-acetylmuramic acid (NAM) and N-acetylglucosamine (NAG), which provide structural integrity and help maintain cell shape.³¹ The inner membrane, which is the second layer, is made up of phospholipids that have multiple functions, such as transport and structural biosynthesis. Additionally, it facilitates sister chromosome separation and acts as a site for DNA anchoring.³² Antibiotic resistance is closely associated with the structural and functional properties of the bacterial outer membrane, particularly in Gram-negative organisms, which influences susceptibility to agents such as β-lactams, quinolones, and colistin. For antibiotics to exert their effect, they must first traverse the bacterial cell envelope to reach their intracellular targets. In this context, hydrophilic compounds typically enter the cell through porin channels, whereas hydrophobic molecules may diffuse directly across lipid components of the membrane. Alterations or mutations in the outer membrane structure can significantly reduce drug permeability, thereby contributing to the development of resistance. Gram-negative bacteria generally exhibit higher levels of intrinsic resistance compared to Gram-positive bacteria, largely due to the presence of this additional outer membrane layer, which is absent in Gram-positive organisms.^33,34 Human sickness is often caused by Gram-negative bacteria, especially in immunocompromised individuals. Gram-negative bacteria cause the most challenging nosocomial infections because of their resistance.³⁵ Vancomycin has much lower affinity than the terminal wild type d-Ala-d-Ala in modified peptidoglycan precursors with a terminal d-Ala-d-Lac, which are produced by Van A genes (Fig. 2).

Fig. 2. Resistance mechanisms found in Gram-positive and Gram-negative bacteria.

5. Other methods for managing MDR infections

Using nanotechnology, anti-MDR-resistant nanobacterial agents are produced. One study suggests using nanoparticles in place of antibiotics and other disinfectants. Silver, zinc, gold, copper, and other inorganic and organic elements can be incorporated into liposome nanoparticles for use as disinfectants and antibiotics. Preventing biofilm formation and catheter-associated urinary tract infections (CAUTI) are two of the most common uses of nanoparticles as antibiotics. Additionally, antimicrobial coatings and bandages for wounds have employed nanoparticles.^36,37 It is easy for bacterial pathogens to develop antimicrobial resistance to a therapeutic treatment because resistance can arise even from simple genetic alterations.³⁸ Therefore, one of the most promising approaches to reducing antimicrobial resistance is the antibiotic combinatorial strategy.³⁹

6. Potential heterocyclic compounds for treating infectious diseases

Because aromatic heterocyclic compounds are present in the side groups of the most common and essential components of all living cells, heterocyclic compounds are important in biological processes.^40,41 These heterocyclic compounds are used as medications in several human and veterinary medications, as well as herbicides and insecticides in agriculture, along with organic compounds that have biological functions. These chemical rings are present in several commercially available medications (Fig. 3).

Fig. 3. Literature survey of antibacterial activity of heterocyclic compounds.

These rings' presence demonstrated that these kinds of medications had pharmacological qualities while also providing a platform for various pharmacophoric groups that can interact with receptors.⁴² By focusing on several bacterial pathways and avoiding typical resistance mechanisms including enzyme inactivation, target mutations, and efflux pumps, heterocyclic scaffolds overcome antimicrobial resistance. For example, thiazoles and beta-lactams covalently target penicillin-binding proteins (PBPs) to impair cell wall formation, while quinoline and fluoroquinolone cores inhibit bacterial DNA gyrase and topoisomerase IV to prevent replication. Advanced heterocycles that interfere with ergosterol biosynthesis, damage bacterial cell membranes, or produce intracellular reactive oxygen species (ROS) include triazoles, imidazoles, and silver-N-heterocyclic carbenes (NHC-Ag). They can defeat MDR bacterial strains, lower sensitivity to efflux transport, and prevent sterically hindered mutant enzymes from binding thanks to their strong hydrogen-bonding capacity, adjustable electron density, and capacity to build bulky or metal-chelating hybrid structures.

6.1. Furan: a promising scaffold for antibacterial activity

Many substituted furan derivatives containing a mono and fused furan in combination with other heterocyclic compounds have been approved for clinical use; a small change in the pattern of substitution can significantly change the biological activity of furans. Furan derivatives have assumed a unique role in the field of medicinal chemistry.^43,44 Among the five-membered heterocyclic compounds, furan is the most reactive. Compared to other chemicals, it requires very weak reagents because of its great reactivity. Furan ring compounds are often good solvents. Certain materials are miscible with water and hexane. Polarity and the potential for hydrogen bonding are increased by the presence of ether oxygen. The addition of the furan nucleus is a crucial synthetic method in the hunt for novel medications. A list of the drugs and their noteworthy pharmacological actions may be seen in Fig. 4, 5, and 6. The great therapeutic efficacy of furan-related medicines has encouraged medicinal chemists to develop several innovative chemotherapy agents (Table 1).⁴⁵

Fig. 4. Clinically approved drugs containing furan ring.

Fig. 5. List of furan ring containing novel drug market.

Fig. 6. List of furan ring containing drug withdrawal from market.

Table 1. Summary of furan derivatives in medicinal chemistry and drug design.

Aspect	Content/analysis
Core subject	Mono- and fused-furan derivatives in medicinal chemistry43,44
Chemical characteristics	High reactivity among 5-membered heterocycles, increased polarity and hydrogen-bonding potential via ether oxygen, high solubility/miscibility properties
Biological significance	Slight changes in substitution patterns significantly alter biological activity
Synthetic utility	Acts as an important core nucleus in drug design; high reactivity permits synthetic functionalization under milder conditions
Clinical relevance	High therapeutic efficacy led to clinically approved drugs and diverse novel chemotherapeutic agents (Fig. 4–6)45

6.1.1. Novel antibacterial agents containing furan in their molecular structure

Furan's biological importance as an antimicrobial agent was determined by creating 3-aryl-3-(furan-2-yl) propionic acid derivatives 1 and evaluating their antibacterial efficacy. Compound 1 produced the greatest results, inhibiting Escherichia coli growth at a MIC of 64 µg mL⁻¹.⁴⁶ The presence carboxylic group Acts as a polar head group that forms key ionic interactions, salt bridges (e.g., with Arg/Lys), and hydrogen bonds within the target active site.^47–49

2,4-Disubstituted furan derivative 2 exhibited better antibacterial activity especially against Proteus vulgaris and Escherichia coli.⁵⁰ NH₂ group: acts as a critical hydrogen-bond donor; modifying or acetylating this primary amine typically diminishes binding affinity and serves as a key binding domain capable of forming strong hydrogen-bonding and hydrophobic interactions within target enzyme active sites (such as kinases or bacterial enzymes).

It was discovered that a novel aryl-furan derivative 3 exhibited significant activity against both Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli) bacteria, suggesting a wide range of action for this novel chemical.⁵¹ The para-chloro group acts as an electron-withdrawing and lipophilic moiety. It enhances target binding affinity and protects against oxidative metabolic inactivation at the para position.

1-Benzoyl-3-furan-2-ylmethyl-thiourea 4 exhibited antibacterial effect against Listeria monocytogenes, Bacillus cereus and Staphylococcus aureus.⁵² Carbonyl group serves as an important hydrogen-bond acceptor. Its presence conjugated to the thiourea nitrogen enhances the acidity of the adjacent NH group, strengthening its potential hydrogen-bonding capability with active-site residues.

The antibacterial activity of compound 5 was evaluated after it was successfully produced. It was discovered that this substance exhibited broad antibacterial efficacy against thirteen different bacterial strains, outperforming tetracycline and streptomycin in the case of Pseudomonas fluorescens.⁵³ The fluorine atoms engage in unique polar-hydrophobic or multipolar interactions (e.g., C–F H–N/O or backbone interactions), while enhancing metabolic stability against oxidative breakdown and increasing overall cell membrane permeability.

A furan-substituted molecule was synthesized and its antibacterial activity evaluated in a different investigation. When compared to ampicillin as the standard, compound 6 in this series was found to be equipotent against Bacillus cereus, Shigella dysenteriae, Klebsiella pneumonia, Staphlococcus aureus, and Staphylococcus epidermidis.⁵⁴N-Methoxymethyl chain CH₂–OCH₃ introduces controlled lipophilicity and additional hydrogen-bond acceptor capacity via the ether oxygen, improving target fitting and pharmacokinetic properties.

Hybrid compounds incorporating the pharmacophoric features of furanones and fluconazole have demonstrated promising antifungal activity. Among these, compound 7 exhibited potent efficacy against Candida albicans and Candida glabrata, with MIC₅₀ values of 0.5 µg mL⁻¹ for both strains. Additionally, it showed notable activity against Candida tropicalis, with an MIC₅₀ value of 2 µg mL⁻¹.⁵⁵

The efficacy of 2-(5-(5-nitrofuran-2-yl)-1,3,4-thiadiazol-2-ylimino) thiazolidin-4-one derivatives against three strains of Helicobacter pylori is evaluated. Strong antibacterial activity was demonstrated by compounds 8a–c against Helicobacter pylori strains (inhibition zone > 30 mm) at 100 µg per disc and (inhibition zone > 20 mm) at 50 µg per disc.⁵⁶

2-(2-Arylidenehydrazineyl)-4-(furan-2-yl)-6-(4-nitrophenyl)pyrimidines, 10 was made by dissolving compound 9 with benzaldehyde in ethanol while using glacial acetic acid as a catalyst. The reaction mixture was refluxed for three to four hours, cooled, and then poured over crushed ice. Filtering, drying, and recrystallizing the ethanol-derived product produced chemical 10. With MICs of 12.5 and 50 µg mL⁻¹, compound 10 demonstrated efficacy against S. aureus and E. coli.⁵⁷

ZnCl₂ was added as a catalyst after thioglycolic acid (TGA) and compounds 10 (0.01 mol) were combined to create a solution. For eight hours, the reaction mass was stirred at 120 °C. After the necessary amount of stirring, the reaction mixture was put to crushed ice and neutralized with NaHCO₃ solution. The final product was filtered, dried, and recrystallized from methanol to obtain compound 11. With MIC values of 50, 62.5, and 25 µg mL⁻¹ when compared to the common medication ciprofloxacin, compound 11 is clearly efficient against the bacterial strains P. aeruginosa, S. aureus, and S. pyogenes.⁵⁸

The effectiveness of derivatives of 3-aryl-3(furan-2-yl) propanoic acid as an antibacterial agent was studied. Compound 12 exhibited the most favourable outcomes, inhibiting Escherichia coli growth at a MIC of 64 µg mL⁻¹.^59,60

Derivatives of furan 2,4-disubstituted 13 demonstrated superior antibacterial activity, particularly against Escherichia coli and Proteus vulgaris comparison with Streptomycin as standard drug.⁶¹

The newly synthesized aryl furan derivative (compound 14) exhibited significant antibacterial activity against both Escherichia coli and Staphylococcus aureus, representative of Gram-negative and Gram-positive bacteria, respectively, suggesting its potential as a broad-spectrum antibacterial agent.⁶²

The antibacterial activity of compound 15 was evaluated after it was successfully synthesized. This substance was discovered to exhibit broad antibacterial activity against thirteen different bacterial strains, outperforming both streptomycin and tetracycline in terms of activity against Pseudomonas fluorescence.⁶³

6.2. Pyrrole: a promising scaffold for antibacterial activity

Numerous pyrrole-containing compounds have been successfully developed into marketed drugs, while others remain under clinical evaluation.⁶⁴ The pyrrole moiety is a key structural feature in several approved pharmaceuticals, including atorvastatin (a representative statin), glimepiride (a sulfonylurea antidiabetic agent), and nonsteroidal anti-inflammatory drugs (NSAIDs) such as ketorolac and tolmetin.^65,66 In addition, it is present in pyrvinium, an anthelmintic agent,⁶⁷ and sunitinib, a widely used chemotherapeutic drug (Fig. 7) and (Table 2).⁶⁸

Fig. 7. Examples of synthetic pharmaceutical drugs containing pyrrole or pyrrole-related heterocyclic rings: (a) atorvastatin; (b) glimepiride; (c) ketorolac; (d) tolmetin; (e) pyrvinium; and (f) sunitinib.

Table 2. Critical evaluation and suggestions for improvement.

Evaluated category	Excerpt content & analysis	Critical evaluation & suggestions for improvement
Pharmacological scope & versatility	Highlights pyrrole as a key pharmacophore across diverse therapeutic areas: lipid-lowering (atorvastatin), antidiabetic (glimepiride), anti-inflammatory (ketorolac, tolmetin), anthelmintic (pyrvinium), and oncology (sunitinib)64–68	Strengths: effectively demonstrates the structural versatility and privilege of the pyrrole ring in drug discovery
		Weaknesses: lists drugs without explaining why pyrrole is utilized (e.g., core scaffold, hydrogen bonding, metabolic stability)
Accuracy of scientific claims	Identifies specific marketed drugs containing pyrrole rings or fused pyrrole systems65–68	Fact check & precision:
		• Glimepiride: contains a pyrroline/pyrrolidone (2-pyrrolidone) ring rather than a simple aromatic pyrrole ring. It is more accurate to clarify this as a pyrrole-derived or pyrrolidinone-containing structure
		• Ketorolac & tolmetin: ketorolac features a fused pyrrolizine nucleus, whereas tolmetin contains a simple 1-methylpyrrole core
Grammar, syntax & style	Short paragraph introducing Fig. 7 (ref. 68)	Issues identified:
		• Sentence fragment/dangling punctuation at the end: (Fig. 7)68
		• Repetitive structure (“In addition, it is present in…”)
Evaluated category	Excerpt content & analysis	Critical evaluation & suggestions for improvement
		• Combine into a cohesive flow: “Notably, the pyrrole scaffold is incorporated into diverse therapeutic classes, including…”
Citation & formatting	Uses ref. 64–68 and refers to Fig. 7	Formatting note: double periods present after citation bracket68 clean up to a single period following standard scientific style guides (e.g., ref. 68)

6.2.1. Novel antibacterial agents containing pyrrole in their molecular structure

Nitrogen-containing heterocyclic compounds, including pyrrole derivatives, have been shown to exhibit notable antibacterial activity against a wide range of both Gram-positive and Gram-negative bacterial strains.⁶⁹ The antibacterial efficacy of pyrrole-based molecules is strongly influenced by the nature and position of substituent groups, with various modifications leading to enhanced biological activity.⁷⁰ Overall, pyrrole-containing scaffolds display a broad spectrum of antibacterial potential, and numerous studies in recent years have reported significant interest in this class of compounds.^71,72

6.2.1.1. Alkaloids

For the creation of optimal derivatives with possible antibacterial action, alkaloids serve as useful natural templates. Based on structure–activity relationship (SAR) analyzes of 4,5-dibromo-N-[4-[3-[(4,5-dibromo-1H-pyrrole-2-carbonyl)amino]propylamino]butyl]-1H-pyrrole-2-carboxamide 16, a di-brominated pyrrole spermidine alkaloid isolated from the marine sponge Pseudoceratina purpurea. Several of the synthesized derivatives showed similar or even greater potency in comparison to pseudoceratidin 1, according to an evaluation of their antibacterial activity, indicating their potential as attractive antibacterial lead compounds.⁷³

Overall, this class of compounds tends to exhibit greater antibacterial activity against Gram-positive bacteria compared with Gram-negative strains. Moreover, systematic structural modifications have facilitated the establishment of a well-defined structure–activity relationship (SAR). The observed potent antibacterial effects are strongly influenced by specific structural features, including dihalogenation of the pyrrole ring. In addition, compounds containing two pyrrole units, particularly those incorporating extended alkyl linkers or one or more secondary amine groups within the side chain, demonstrated enhanced antibacterial potency. Furthermore, derivatives with longer carbon chains are suggested to possess improved ability to penetrate bacterial cell membranes, thereby contributing to increased biological activity.⁷⁴

6.2.1.2. Armeniaspirols and derivatives

Investigation of the complex structures of armeniaspirol natural products enabled the synthesis of a series of chemical derivatives through demethylation and dechlorination reactions. This approach led to the identification of nine novel armeniaspirol analogues, providing important insights into the role of methyl and chlorine substituents on the pyrrole framework in modulating antibacterial activity. When compared to their chlorinated and methylated counterparts, the derivatives N-desmethyl armeniaspirols A–C and 9-deschloro armeniaspirols A–C shown decreased antibacterial activity against Bacillus subtilis, Enterococcus faecium, and Enterococcus faecalis. These findings imply that the presence of both methyl and 9-chloro substituents considerably affects the antibacterial effectiveness of pyrrole-based systems.⁷⁵

6.2.1.3. Pyrrolyl benzamide derivatives

A series of novel pyrrole–benzamide derivatives (18a) was synthesized and evaluated for their inhibitory activity against enoyl-acyl carrier protein reductase (InhA), an essential enzyme involved in type II fatty acid biosynthesis in Mycobacterium tuberculosis. The compounds were also assessed for their antitubercular activity against M. tuberculosis H37Rv and their ability to inhibit InhA. Among the tested derivatives, N-(2-nitrophenyl)-4-(1H-pyrrol-1-yl)benzamide (18b) exhibited strong hydrogen-bonding interactions within the InhA active site, indicating favorable binding affinity. In vitro antitubercular screening revealed that derivatives bearing substituents such as 4-ClC₆H₄, 3-FC₆H₄, 2,3-ClC₆H₃, 2-NH₂C₆H₄, and compound 18b showed the highest activity, with a minimum inhibitory concentration (MIC) of 3.125 µg mL⁻¹. This activity was compared with standard drugs isoniazid (MIC = 0.25 µg mL⁻¹) and triclosan (MIC = 10 µg mL⁻¹). Furthermore, five selected compounds were evaluated for antibacterial activity, where they exhibited greater potency against Staphylococcus aureus than against Escherichia coli, with MIC values ranging from 3.12 to 12.5 µg mL⁻¹, using ciprofloxacin (MIC = 2 µg mL⁻¹) as the reference drug. Overall, pyrrole–benzamide derivatives demonstrate promising potential as lead scaffolds for the development of InhA inhibitors and novel antibacterial agents.⁷⁶

6.2.1.4. Pyrrole-2-carboxylate and pyrrole-2-carboxamide derivatives

The pyrrole-2-carboxylate scaffold has been identified as a key pharmacophoric element in a series of potential antibacterial derivatives. Four compounds derived from 1H-pyrrole-2-carboxylate were synthesized in this context, and their efficacy against Mycobacterium tuberculosis H37Rv was assessed. Among them, ethyl-4-{[-(1-(2-(4-nitrobenzoyl) hydrazono)ethyl]}-3,5-dimethyl-1H-pyrrole-2-carboxylate (19) displayed a considerable inhibitory effect, with a MIC value of 0.7 µg mL⁻¹, which is equivalent to that of the reference medication ethambutol (MIC = 0.5 µg mL⁻¹). Additionally, all synthesized derivatives showed antibacterial activity against Staphylococcus aureus, although with higher MIC values compared to the standard antibiotic ceftriaxone.⁷⁷ Beyond their antibacterial potential, the pyrrole-2-carboxamide moiety is recognized as an important pharmacophore in medicinal chemistry, contributing to a range of biological activities, including antibacterial, antibiofilm, and antifungal effects, and serving as a crucial structural component in many bioactive compounds.⁷⁸

In this study, novel antimicrobial compounds were designed with the ability to target multiple bacterial species. Notably, the emergence of resistance-conferring mutations against these agents was rare, with only minimal impact on compound susceptibility, while still significantly impairing bacterial growth. The rational design of balanced multi target antibiotics resulted in the development of two new chemical entities within a distinct structural class: ULD1, found to be (2-(3,4-dichloro-5-methyl-1H-pyrrole-2-carboxamido)benzo[d]thiazole-6-carboxylic acid (20a), while ULD2 was found to be (4-(benzyloxy)-2-(3,4-dichloro-5-methyl-1H-pyrrole-2-carboxamido)benzo[d]thiazole-6-carboxylic acid (20b).⁷⁹

6.2.1.5. Pyrrole-3-carboxaldehyde derivatives

The synthesis of highly substituted pyrrole-3-carboxaldehydes was achieved via reaction between an aromatic aldehyde and a protected amine. Among the synthesized compounds, three selected derivatives exhibited notable antibacterial activity against Pseudomonas putida, with an MIC value of 16 µg mL⁻¹, which was comparable to the standard antibiotic chloramphenicol. (21a) 1-(4-Methoxyphenyl)-5-phenyl-2-(pyridin-3-yl)-1H-pyrrole-3-carbaldehyde, (21b) 1-(4-methoxyphenyl)-5-phenyl-2-(pyridin-4-yl) (21c) and -1H-pyrrole-3-carbaldehyde 1-(4-methoxyphenyl)-5-phenyl-2-(thiophen-2-yl)-1H-pyrrole-3-carbaldehyde.⁸⁰

A series of novel O-acyloxime derivatives of 4-formylpyrroles, namely 5-chloro-4-({[alkyl (aryl)oxyimino]methyl})-1H-pyrrole-3-carboxylates, was synthesized and evaluated for their antibacterial activity. These compounds exhibited broad-spectrum antimicrobial effects against Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Klebsiella pneumoniae, Staphylococcus epidermidis, Corynebacterium xerosis, and Enterococcus faecalis, with MIC values ranging from 7.81 to 125 µg mL⁻¹. Notably, compound 22 (ethyl 5-chloro-2-methyl-1-propyl-4-[({[4-(pyrrolidin-1-ylsulfonyl) benzoyl]oxy}imino)methyl]-1H-pyrrole-3-carboxylate) demonstrated strong activity against Proteus mirabilis, with an MIC value of 7.81 µg mL⁻¹, which was superior to the reference antiseptic Decasan (decamethoxin, MIC = 15.625 µg mL⁻¹).⁸¹

A new series of 2-amino-1,5-diaryl-1H-pyrrole-3-carbonitrile derivatives was synthesized and evaluated for antibacterial activity. The compounds demonstrated strong inhibitory effects against Staphylococcus aureus, while showing no activity against Escherichia coli. In particular, 2-amino-1-phenyl-4-(pyridin-4-ylamino)-5-(p-tolyl)-1H-pyrrole-3-carbonitrile (23) exhibited potent antibacterial activity against Staphylococcus aureus, with an MIC value comparable to the reference drug gentamicin (0.008 µM). Furthermore, this compound showed significant DNA gyrase inhibitory activity, with an IC₅₀ value of 0.0236 ± 0.45 pM, which was slightly higher than that of gentamicin (0.02323 ± 0.81 pM).⁸²

6.2.1.6. Pyrrole-based chalcone derivatives

Chalcones represent promising natural scaffolds for the discovery and development of novel anti-infective agents, as numerous studies have reported their significant antibacterial and antifungal activities, including effectiveness against resistant strains.^83,84 In this context, a series of pyrrole-based chalcones (24a–c) was designed and synthesized via the condensation of 2-acetyl-1-methylpyrrole with 5-(aryl) furfural derivatives.

6.2.1.7. Pyrrolo-pyrimidine derivatives

A series of novel pyrrolo[2,3-d]pyrimidine derivatives (25) was synthesized and evaluated for their antibacterial activity. When compared with the standard antibiotic gentamicin, several of the newly prepared compounds exhibited promising antibacterial properties. In particular, with a minimum inhibitory concentration (MIC) of 0.5 µg mL⁻¹, the derivative 6-(4-bromophenyl)-3-[2-(2-hydroxyethoxy)ethyl]-7-phenyl-3,7-dihydro-4H-pyrrolo [2,3-d] pyrimidin-4-one had the strongest action against Salmonella enteritidis and Escherichia coli.⁸⁵

Several series of substituted pyrroles along with their fused pyrimidine and triazine derivatives were synthesized and evaluated for antibacterial activity. In general, both Gram-positive (Staphylococcus aureus and Bacillus subtilis) and Gram-negative (Escherichia coli and Pseudomonas aeruginosa) bacteria were inhibited in their growth by the produced chemicals. Four compounds showed greater action against Gram-positive bacteria than ciprofloxacin, with lower MIC values and broader zones of inhibition. The most active derivative was 7-(4-chlorophenyl)-8,9-diphenyl-6,7-dihydro-2H-imidazo[1,2-c]pyrrolo[3,2-e]pyrimidine-5(3H)thione (26), which showed a zone of inhibition similar to ciprofloxacin with a lower MIC against Escherichia coli and an equivalent MIC against Pseudomonas aeruginosa.⁸⁶

Phenyl derivatives bearing ortho- or meta-substituents may facilitate improved penetration into bacterial cells and enhance proper binding to biological targets. In contrast, the presence of a fluorine substituent appears to negatively affect antitubercular activity. Comparative analysis between compounds containing an unsubstituted phenyl ring and those substituted at the para position with either a morpholino or phenoxy group revealed that the unsubstituted and phenoxy-substituted analogues generally exhibited good to excellent antitubercular activity. Among the evaluated compounds, the derivative N-(4-phenoxyphenyl)-7H-pyrrolo [2,3-d] pyrimidin-4-amine (27) emerged as the most potent candidate, displaying a MIC₉₀ value of 0.488 µM.⁸⁷

Six novel bicyclic trifluoromethylated pyrrole derivatives were designed and synthesized, and their in vitro antibacterial activities were evaluated against Staphylococcus aureus, Escherichia coli, and Acinetobacter baumannii. Among the tested compounds, 2,2,2-trifluoro-1-[(2R)-2-hydroxy-7-(trifluoromethyl)-2,3-dihydro-1H-pyrrolizin-5-yl]ethanone (28a) and 2,2,2-trifluoro-1-[7-(trifluoromethyl)-2,3-dihydro-1H-pyrrolizin-5-yl]ethanol (28b) showed strong antibacterial action, especially against bacterial strains that were resistant to multiple drugs.⁸⁸

A series of thiazolyl-halogenated pyrrole and pyrazole derivatives was designed and synthesized as potential antibacterial and antibiofilm agents. Among the tested compounds, 2-bromo-6-(2-(3,4,5-tribromo-1H-pyrrol-2-yl)thiazol-4-yl)-4-(trifluoromethyl)phenol (29) showed notable antibacterial activity against several Gram-positive bacteria, particularly exhibiting strong efficacy against vancomycin-resistant Enterococcus faecalis with an MIC value of ≤0.125 µg mL⁻¹ comparison with ampicillin as standard drug. In addition, at sub-inhibitory concentrations, this compound significantly inhibited biofilm formation by Pseudomonas aeruginosa and Staphylococcus aureus, indicating its potential as a promising antibiofilm agent.⁸⁹

Recently, 1,2,3-triazole and isoxazole rings have been successfully hybridized with the antibacterial scaffold 4,5-dibromopyrrole. In this context, a series of novel 4,5-dibromo-N-phenyl-1H-pyrrole-2-carboxamide derivatives 30, 31 incorporating substituted triazole and isoxazole moieties was designed and synthesized as potential inhibitors of Escherichia coli DNA gyrase. Among the prepared hybrids, four compounds exhibited promising DNA gyrase inhibitory activity. Molecular docking studies were also performed to elucidate the binding interactions between the hybrids and the target enzyme. Overall, the antibacterial evaluation indicated that these derivatives were more effective against Gram-negative bacteria compared with Gram-positive strains.⁹⁰

6.3. Thiophen: a promising scaffold for antimicrobial activity

Heterocyclic compounds containing nitrogen and sulfur play a pivotal role in medicine, particularly in cancer treatment and antimicrobial development, due to their ability to form hydrogen bonds, increase stability, and interact effectively with biomolecules, leading to several FDA-approved antibiotics (Fig. 8).⁹¹

Fig. 8. Cefoxitin: a second-generation cephamycin (often grouped with cephalosporin) antibiotic used to treat a wide variety of bacterial infections, particularly against Gram-negative bacteria and anaerobic bacteria. Sertaconazole: a wide-spectrum imidazole antifungal agent used to treat skin infections such as athlete's foot (tinea pedis).

Recent research highlights the remarkable antimicrobial efficacy of Ag(i) and Au(i) complexes against antibiotic-resistant pathogens,⁹² with Ag(i)-tazobactam showing enhanced broad-spectrum activity compared to tazobactam alone.⁹³ Furthermore, silver-N-heterocyclic carbene (NHC-Ag(i)) complexes, especially those featuring quinoline-based ligands or alkanol N-functionalization, have demonstrated superior antibacterial potency compared to existing silver-based drugs.^94,95 The text also notes that while gold complexes historically served as antimicrobials in medieval alchemy (aurum vitae),⁹⁶ their prominence waned with the discovery and mass production of penicillin 97, before concluding with Fig. 8, which illustrates various marketed drugs featuring the thiophene ring scaffold (Table 3).

Table 3. Critical analysis of marketed thiophene-containing drugs.

Drug name	Pharmacological class	Mechanism of action/target	Structural role of thiophene scaffold	Primary clinical application & critical notes
Plavix® (Clopidogrel)	Antiplatelet/thienopyridine prodrug	Irreversible P2Y12 ADP receptor antagonist on platelets	The tetrahydrothienopyridine core is bioactivated by hepatic CYP450 to expose a active thiol group that covalently binds P2Y12	Prophylaxis of thromboembolic events (stroke, MI)
				Critical aspect: requires metabolic activation; CYP2C19 poor metabolizers show reduced efficacy
Zyprexa® (Olanzapine)	Atypical antipsychotic	Antagonist at dopamine D2 and serotonin 5-HT2A receptors	Fused thienobenzodiazepine core acts as an isostere to dibenzodiazepine (clozapine), maintaining binding affinity while altering metabolic clearance	Schizophrenia and bipolar I disorder
				Critical aspect: high metabolic side-effect profile (weight gain, dyslipidemia) despite improved extrapyramidal safety
Trusopt® (Dorzolamide)	Carbonic anhydrase inhibitor	Selective inhibition of ocular carbonic anhydrase II (CA-II)	Fused thienothiazine-1,1-dioxide ring provides spatial alignment and hydrophobic interactions within the CA-II active site	Glaucoma and ocular hypertension
				Critical aspect: reduces aqueous humor secretion; local administration lowers systemic adverse effects
Zyflo® (Zileuton)	Anti-inflammatory/leukotriene inhibitor	Selective 5-lipoxygenase (5-LOX) enzyme inhibitor	Benzo[b]thiophene scaffold provides hydrophobic interactions, positioning the hydroxyurea moiety to chelate the catalytic active-site iron ($Fe{3+}$)	Prophylaxis and chronic treatment of asthma
				Critical aspect: effectively blocks leukotriene production; requires hepatic enzyme monitoring due to hepatotoxicity risks
Surgam® (Tiaprofenic acid)	Nonsteroidal anti-inflammatory (NSAID)	Non-selective cyclooxygenase (COX-1/COX-2) inhibitor	2-Thiophenecarboxylic acid moiety mimics the phenyl ring in traditional NSAIDs (e.g., ketoprofen), enhancing COX active-site binding	Rheumatoid arthritis, osteoarthritis, and acute inflammation
				Critical aspect: demonstrates potent analgesic and anti-inflammatory activity, though long-term use can cause severe cystitis
Duloxetine (Cymbalta®)	SNRI antidepressant	Dual serotonin and norepinephrine reuptake inhibitor	2-Thienyl ring acts as a bioisostere for an aryl group, optimizing transporter selectivity and lipophilicity	Major depressive disorder, neuropathic pain, fibromyalgia
				Critical aspect: broad clinical indication profile due to dual receptor modulation and favorable target binding kinetics

6.3.1. Novel antibacterial agents containing thiophen in their molecular structure

By stirring 1. HPF₆ with Ag₂O in acetonitrile for a whole night at room temperature, the silver complex 32 was immediately created and extracted with a 77% yield. In a similar manner, silver complex 33 was made from 2. Ag₂O and HPF6 were produced with a yield of 76.14%. The equivalent silver complexes 32 and 33 underwent a carbene-transfer reaction with (SMe₂) AuCl in acetonitrile to yield the gold complexes 34 and 35.⁹⁸ Mechanism investigations showed that complex 35 specifically kills membranes by altering the ATP pool and causing membrane breakdown. Furthermore, Au–NHC complexes were proposed as β-lactamase inhibitors by molecular docking research (Fig. 9).

Fig. 9. By disturbing membrane integrity and ATP pools, inhibiting β-lactamase, and demonstrating potential as novel therapies to combat antibiotic resistance, the novel Au(i) NHC complex demonstrates high action against ampicillin-resistant S. aureus.

By reacting the hydrazine function with 1,3-dicarbonyl compounds (such as acetylacetone, ethyl acetoacetate, diethyl malonate), ethyl cyanoacetate, and 1,2-dichloroethane, a series of thiophene-substituted pyridines derived from 6-(3,4-dimethylphenyl)-2-hydrazinyl-4-(thiophen-2-yl)-pyridine-3-carbonitrile.⁹⁹ Compound 37 demonstrated the strongest antibacterial activity in this series against S. aureus (42% of the activity of gentamicin) and S. typhimurium (59% of the activity of ketoconazole), while compound 36 was the most effective against fungal strains Aspergillus flavus (69% of the activity of ketoconazole), Candida albicans (75% of the activity of ketoconazole), and Gram-negative bacteria E. coli (43% of the activity of gentamicin). The series had no compounds that were effective against B. subtilis.

Recently the reaction of 3-cyanoacetyl indole with ethyl isothiocyanate and KOH in dimethyl-formamide offered the salt intermediate which was transformed into the equivalent ethylthioacetanilide derivative upon treatment with 10% HCl at room temperature. In turn, reaction of ethylthioacetanilide with chloroacetone in absolute ethanol and in catalytic triethylamine at refluxing temperature give the corresponding compound 38 Also, in the same manner ethylthioacetanilide reacted with α-haloketones derivatives furnished the matching thiophene derivatives 39. Compound 38 showed considerable antimicrobial activities towards S. aureus (22 mm), E. coli (25 mm) and C. albicans (24 mm). Also thiophene 39 exhibited antimicrobial activities against all test microbes with inhibition values of 23, 26, 25 and 32 mm against S. aureus, E. coli, C. albicans and A. niger, respectively.¹⁰⁰

6.4. Pyridine: a promising scaffold for antibacterial activity

Nitrogen-containing heterocyclic are greatly effective structures for recognizing bioactive compounds in pharmaceuticals and agrochemicals. Important biological interactions between the pyridine core and receptor sites take place. In addition to H-bonding, the pyridine ring can interact with metal ions or prosthetic groups in biological targets through π–π stacking and chelation, which concurrently increases the binding affinity and selectivity.¹⁰¹ Furthermore, pyridine medications are known to enhance the physiochemical characteristics of native medications due to their pharmacokinetic characteristics. Drugs' (a) metabolic stability, (b) permeability, (c) potency, and (d) binding are all known to be enhanced by pyridine motifs. Pyridine plays a significant function in coordination complexes as a ligand or as an organic solvent.¹⁰² Numerous natural products, including vitamins, alkaloids, and coenzymes, as well as numerous medications (Fig. 10) and insecticides, include the pyridine nucleus. The bioactive molecule's extra heterocycle, in contrast to the pyridine one, was advantageous since it enhanced the antibacterial and antiviral compounds' medicinal qualities and expanded their range.¹⁰³

Fig. 10. Drugs containing pyridine ring.

6.4.1. Novel antibacterial agents containing pyridine in their molecular structure

One pot reaction of cyanoacetohydrazide (1 mmol, 0.99 g), malononitrile (1 mmol, 0.66 g), and aromatic aldehyde, such as 3, 5-dimethoxy benzalidehyde, in absolute ethanol (25 mL) with a catalytic amount of piperidine produced 1,6-diamino-4-(3,5-dimethoxyphenyl)-2-oxo-1,2-dihydropyridine-3,5-dicarbonitrile 40. With a minimum inhibitory concentration (MIC) of 64 µg mL⁻¹, this chemical had the strongest action against Salmonella typhimurium and Pseudomonas aeruginosa.¹⁰⁴

7. Structure activity relationships (SAR)

In order to maximize target affinity and get around bacterial resistance mechanisms, the structure activity relationship (SAR) of heterocyclic antimicrobial agents targeted against multidrug-resistant (MDR) bacteria centers on optimizing the heterocycle's electronic properties, lipophilicity, and hydrogen-bonding capabilities. Triazoles, thiazoles, quinolones, or imidazoles are examples of core rings that incorporate heteroatoms (such as nitrogen, sulfur, or oxygen) to control electron distribution and spatial conformation. This enhances specific binding to bacterial targets, such as DNA gyrase, penicillin-binding proteins (PBPs), or cell membrane enzymes. According to SAR studies, adding halogenated or electronegative substituents (like para-fluorine or chlorine) and modifying lipophilicity (usually keeping an intermediate (log P range of 3–5) greatly improves bacterial membrane penetration and metabolic stability without increasing cytotoxicity to host cells. Additionally, hydrogen bonding and salt-bridge interactions with bacterial active-site residues are strengthened by hybridizing heterocyclic frameworks with lipophilic, hydrophobic, or chelating pharmacophores. This allows these modified structures to interfere with nucleic acid replication in strains resistant to conventional antibiotics, disrupt membrane integrity, or inhibit cell wall synthesis.

8. Recent developments regarding AI-assisted drug discovery

Over the past two to three years, the landscape of antimicrobial research against multidrug-resistant (MDR) bacterial pathogens has undergone a major paradigm shift through data-driven computational strategies, new intracellular drug targets, and next-generation combination regimens. Artificial intelligence (AI) and machine learning platforms have fundamentally accelerated early-stage discovery by evaluating complex structure–activity relationships to identify novel non-traditional heterocyclic scaffolds such as halicin and abaucin that disrupt bacterial cell envelope functions through unexplored mechanisms. Concurrently, structural medicinal chemistry has addressed critical clinical gaps by introducing novel non-β-lactam heterocyclic β-lactamase inhibitors, notably modern diazabicyclooctane (DBO) derivatives like durlobactam and bicyclic boronates such as taniborbactam, which possess potent broad-spectrum activity spanning both serine- and zinc-dependent metallo-β-lactamases (MBLs). In parallel, target selection has expanded beyond classic cellular machinery to previously untargeted structures, highlighted by macrocyclic peptides like zosurabalpin that selectively block lipopolysaccharide transport via the LptB₂FGC complex in carbapenem-resistant Acinetobacter baumannii. Furthermore, structural integration of heterocyclic scaffolds into antimicrobial peptides (AMPs) via backbone stapling, alongside hybrid combinations and efflux pump inhibitors, continues to suppress single-target resistance pathways. Although clinical translation still faces hurdles regarding outer-membrane permeability constraints, organ clearance, and synthetic scaling, these recent advances collectively mark a transformational era in reviving antibacterial pipeline efficacy against priority pathogens.^105,106

9. Future prospects and challenges

Antibiotics have played a transformative role in the prevention and treatment of bacterial infections and continue to hold great therapeutic importance. Nevertheless, the rapid increase in bacterial resistance has introduced significant challenges in the clinical management of infectious diseases. After decades of extensive antibiotic use, the emergence of resistance has become unavoidable, while the spread of multidrug-resistant (MDR) bacteria represents a major threat to global public health. In response, researchers have focused on optimizing the clinical use of antibacterial agents and employing combination therapies with different mechanisms of action to minimize the development of resistance. Despite numerous attempts to overcome bacterial resistance, the discovery of novel antibacterial chemical entities, particularly those acting through new mechanisms, remains the most effective strategy for expanding therapeutic options. Since many currently used antibiotics were originally derived from natural sources, increasing attention has been directed toward the identification of thiophene derivatives from plant materials and the biosynthesis of novel thiophene-based compounds using microorganisms. Such approaches offer considerable potential for the discovery of new antimicrobial agents and promising lead compounds for future drug development. In addition, the development of antibacterial agents targeting key bacterial enzymes involved in essential cellular and metabolic processes has emerged as an important research strategy. This mechanism-based approach to antibacterial drug discovery should continue to be explored and encouraged in future studies. Although most efforts in antimicrobial drug development are centered on organic molecules, organic–inorganic hybrid compounds should not be neglected, as several reports indicate that metal complexes may exhibit stronger antimicrobial activity than the corresponding parent ligands. However, the potential toxicity associated with both the organic ligands and the metal ions must be carefully evaluated during the development of metal-based therapeutics. Overall, the continued exploration of scaffolds and their modified analogues is expected to inspire medicinal chemists in the design of innovative therapeutic agents. Such structural diversity may contribute significantly to the future discovery of effective antimicrobial compounds with enhanced pharmacological properties and novel mechanisms of action.

10. Conclusion

The discovery of antibiotic and antibacterial agents has greatly enhanced the quality of healthcare for both humans and animals, transforming the management of bacterial infections during the antibiotic “golden age” over the last half-century. Nevertheless, the extensive utilization of these agents in clinical medicine, veterinary applications, agriculture, food processing, and industrial activities such as ethanol production has contributed to the accumulation of antibiotics in the environment. This environmental exposure disrupts beneficial microbial communities and promotes the emergence and spread of resistant bacterial strains, ultimately posing a major challenge to global health systems.

Consequently, addressing antimicrobial resistance requires collaborative action from all stakeholders, including healthcare professionals, the pharmaceutical industry, policymakers, and the public, to encourage the responsible and rational use of antimicrobial drugs and to raise awareness regarding the risks associated with resistant pathogens.

At the same time, the broad structural diversity provided by heterocyclic compounds and their derivatives offers extensive opportunities for the development of novel therapeutic agents. The versatility of heterocyclic scaffolds enables medicinal chemists to design molecules with improved selectivity and target specificity. Recent trends in newly approved pharmaceuticals further emphasize the increasing importance of heterocyclic moieties in modern drug discovery. Therefore, continued exploration of heterocycle-based pharmacophores is expected to play a significant role in the development of future pharmacologically active compounds with diverse therapeutic applications.

Conflicts of interest

No conflict of interest is associated with this work.

Data availability

No primary research results have been included and no new data were generated or analysed as part of this review.