Natural products against gram-negative bacteria: promising antimicrobials in future complementary medicine

Abstract

Gram-negative bacteria are nonfermentative and opportunistic and are among the most important causes of nosocomial infections. These bacteria, especially Pseudomonas aeruginosa, Acinetobacter baumannii and Escherichia coli, are resistant to various antibiotics worldwide. This level of antibiotic resistance as well as the overuse of drugs can be among the most important reasons for the tendency toward naturally occurring products. Although the majority of natural products have much greater antibacterial activity against gram-positive bacteria than gram-negative ones, in this review, we presented natural products with anti-gram-negative bacteria and their mechanisms of action. Phenolic compounds, terpenoids, alkaloids and organosulfur compounds are among the most important classes of antimicrobial natural products and are briefly discussed.

Introduction

Bacteria are among the most important and diverse microorganisms that can be useful in the life cycle and can also cause many diseases in the human body and other organisms. Some bacteria have surface structures or molecules that increase their ability to attach to host cells. For example, some gram-negative bacteria have cells that enable them to attach to the membranes of the gastrointestinal tract or genitourinary tract. Pathogens generally use a variety of ways to escape destruction by a specific immune system. Many pathogens are safe during immune attack due to their ability to grow in host cells or reduce their antigenicity by shedding membrane antigens. Other pathogens disguise themselves from the immune system by mimicking the surface of host cells. Many pathogens can selectively suppress or suppress the immune response by activating an arm of the immune system that is not effective against the pathogen (Lotte et al. 2016). Despite the availability of a large number of antibiotics and the multimillion-dollar pharmaceutical industry, there is still a long way to go before bacteria can be eliminated. One of the main reasons for this is the resistance of many bacteria, especially gram-negative bacteria, to the effects of antibiotics. If the selected antibiotic is unable to achieve its goal due to a lack of penetration into the blood–brain barrier or lack of penetration into the abscess, it can lead to treatment problems (Mazzariol et al. 2017). Other problems are related to the concentration of antibiotics. In some cases, antibiotics are rapidly excreted and metabolized, and thus, their levels in the blood are reduced. This makes antibiotic treatment ineffective when the infectious agent needs to be exposed for a long time to a high level of antimicrobial medication to eliminate it. In other cases, antibiotics are rapidly absorbed into a specific tissue or organ, and other areas of infection may have relatively little access to antibiotics. Gram-negative bacteria develop resistance to antibiotics through a variety of mechanisms, which can pose major challenges to the spread and treatment of some infectious agents (Shorr 2009; Le Doare et al. 2015). High resistance to antibiotics causes difficulty in treating infections caused by these infections. Secondary metabolites could be one of the best option for controlling gram-negative bacteria, the advantages of which include low production costs and low side effects (Esmaeilzadeh kashi et al. 2023; Hamidi et al. 2024). In this review, we will discuss some of the natural antibacterial compounds used against gram-negative bacteria as promising antibiotics in future complementary medicine.

Methodology

In this review, extensive surveys of “natural products”, “terpenoids”, “secondary metabolites”, “alkaloids”, “phenolics”, “antimicrobial”, and “gram-negative” were conducted in scientific databases, including the Web of Science, Pubmed, Scopus, Reaxys, and Google Scholar. The articles that included reports of the isolated compounds with antibacterial activity were used for data collection. To identify more articles, the reference lists of the included studies were also explored. Moreover, articles focused on synthetic antibacterial natural products were excluded from this review. Approximately two hundred thirty-two publications met our inclusion criteria for collecting the present information.

Prokaryotic cell architecture

Bacteria are a group of microscopic single-celled organisms that are surrounded by a relatively thick outer covering (Spitzer 2011). These organisms have simple structures and belong to the group of prokaryotes (simple organisms). They are very small organisms, and their unit of measurement is microns. The normal size of bacteria with independent metamorphosis is 1 to 5 microns, but their size range can be considered to be 1–15 microns. Bacteria are classified according to staining (gram-negative or positive), shape (cocci, bacilli, coco bacilli, Vibrio, spiral and spirochetes), and metabolism (anaerobic, aerobic, optional anaerobic, etc.) (Davis and Park 1962; Huws et al. 2011). Bacterial cells, like other cells, are composed of the nucleus, cytoplasm, and membrane, as well as the bacterial cell wall. Bacteria multiply by direct division, fusion, fragmentation, or conidia, as well as germination (Driks 2002). For the purpose of this review article, we will continue to study gram-negative bacteria.

Gram-negative bacteria

A gram-negative cell cover is a multilayered and very complex structure. The cytoplasmic membrane (called the inner membrane in gram-negative bacteria) is covered by a flat sheet of peptidoglycan to which a complex layer called the outer membrane attaches (Beveridge 1999). An external capsule or S layer may also be present. The space between the inner and outer membranes is called the periplasmic space (Costerton et al. 1974). In gram-negative bacteria, the number of peptidoglycan layers is low and can reach three. The cell wall of gram-negative bacteria has three components located in the outer layer of peptidoglycan: a lipoprotein, an outer membrane and a lipopolysaccharide (Silhavy et al. 2010). The outer membrane has two layers whose outer surface contains lipopolysaccharide (LPS) (Vanaja et al. 2016; Good et al. 2000). This membrane protects bacteria against harmful substances such as bile salts, which are large molecules also known as lipoglycans and endotoxins, in the intestine (Seid et al. 1980; Betanzos et al. 2009). These molecules are found in the outer membrane of gram-negative bacteria and produce strong immune responses. Lipopolysaccharide (LPS) is composed of three components: antigen O, central oligosaccharide (up to 20 bonds) and lipid A. LPS has two lipid and polysaccharide moieties; the lipid moiety is the same as that of lipid A, and the polysaccharide moiety contains the O antigen and core fixed sugar (Shands 1971; Gutsmann et al. 2000). In gram-negative bacteria, LPS contains lipid-A. Lipid-A is essential for the function of many foreign membrane proteins. As long as this lipid is in the wall, it does not have febrile properties, but when the bacterial wall is destroyed, this lipid is released to the brain, causing an increase in body temperature and fever by acting on the hypothalamus (Kato et al. 1985). Lipopolysaccharides are highly toxic to animals and are called endotoxins (Kato et al. 1985). Lipoprotein binds peptidoglycan layers and membranes together to stabilize the outer membrane (Fig. 1). Antigen O may even differ between different strains of bacteria, but the structure of the core sugar in gram-negative bacteria is the same. Lipoproteins in gram-negative bacteria have a two-part structure. The protein is attached to peptidoglycan, and the lipid is attached to the outer membrane. Purines are special proteins that pass through cell membranes and act as a pore through which molecules can be released. Purines contain families of proteins found in the outer membrane of gram-negative bacteria. Many gram-negative bacteria, especially Acinetobacter, Pseudomonas, and Escherichia coli, are bacteria that have historically exhibited high resistance to various microbial agents (Nikaido 1996). Gram-negative bacteria develop resistance to antibiotics through a variety of mechanisms, which can pose major challenges to the spread and treatment of some infectious agents. High resistance to antibiotics causes difficulty in treating infections caused by these infections. In the following, we will discuss the mechanism of antibiotic resistance in gram-negative bacteria samples (Nikaido 1996).

Fig. 1

An illustration of the cell wall structure in gram-negative bacteria

Pattern of antibiotic resistance

Despite the availability of a large number of antibiotics and the multimillion-dollar pharmaceutical industry, there is still a long way to go before bacteria are eliminated (Schober et al. 2010). The suitable effectiveness of an antibiotic occurs when the antibiotic reaches the appropriate concentration and maintains that concentration for a sufficient period of time (Ehinmidu 2003; Mulu et al. 2006). Bacterial resistance to various antibiotics is one of the greatest challenges that threatens human health in the modern era. The ability of microbes to undergo genetic changes is not the only reason for antibiotic resistance, and various mechanisms are effective in creating drug resistance. Antibiotic resistance also affects agriculture and the environment. Other problems are related to the concentration of antibiotics. In some cases, antibiotics are rapidly excreted and metabolized, and thus, their levels in the blood are reduced (Shomura and Umemura 1973; Kenny and Strates 1981). This makes antibiotic treatment ineffective when the cause of the infection needs to be exposed for a long time to a high level of antimicrobial medication. In other cases, antibiotics are rapidly absorbed into a particular tissue or organ, and other areas of infection may have relatively little access to antibiotics (Naamala et al. 2016). Bacteria become resistant to antibiotics in at least three common ways. Some bacteria produce enzymes that inactivate antibiotics by adding a group (methyl, acetyl, or phosphate) or breaking a key junction (such as the beta-lactam ring in penicillins). For example, penicillin G-resistant staphylococci produce the enzyme beta-lactamase, which breaks down the drug. Gram-negative bacteria resistant to aminoglycosides (plasmid-mediated) produce adenylation, phosphorylation or acetylating enzymes (El-Halfawy and Valvano 2012). Second, by altering permeability, some bacteria become relatively resistant to antibiotics, which is mostly due to changes in purine molecules or LPS components. Changes in lipopolysaccharides affect drug permeability by altering the cell surface charge. For example, in the case of tetracycline resistance, drug withdrawal from the cell is greatly increased. Resistance to polymyxins is also due to changes in drug permeability. Streptococci exhibit inherent resistance to aminoglycosides (Sirichoat et al. 2020). This permeability is overcome by the simultaneous presence of a cell wall-destroying drug such as penicillin. Resistance to amikacin and other aminoglycosides may be due to drug permeability (El-Halfawy and Valvano 2012). For example, staphylococci become resistant to methicillin when penicillin-binding proteins (PBPs) lose their tendency to bind to methicillin, or some types of E. coli become resistant to streptomycin due to changes in the S12 protein (Hartman and Tomasz 1981). In most cases, bacteria contain extra chromosomal agents called plasmids. Some plasmids carry genes that target one or more antimicrobial drugs (Blair et al. 2015). Plasmid genes for antimicrobial resistance are often capable of degrading antimicrobial drugs. Thus, plasmids determine the extent of resistance to penicillins and cephalosporins by carrying genes that produce beta-lactamases. Transmission occurs through transduction, transformation and conjugation (Chapman 2003; Wilson 2014). A wide range of natural and chemical compounds are used as antimicrobial agents. The widespread and incorrect use of antibacterial compounds has caused the emergence of pathogens resistant to antimicrobial compounds as a serious threat to global health. Briefly, antimicrobial agents work via different methods, such as inhibition of cell wall synthesis, inhibition of cell membrane synthesis, inhibition of protein synthesis and inhibition of nucleic acid synthesis in bacteria.

The most important gram-negative resistant bacteria

Enterobacteriaceae

Enterobacteriaceae are a large group of gram-negative bacteria without spores. These bacteria are aerobic, anaerobic or facultative anaerobic organisms found in soil, water and plants as well as part of the natural gut flora of humans and animals (Edwards and Ewing 1972). These bacteria grow on normal laboratory media such as bloody nutrient agar (Paruch and Mæhlum 2012). Some of these organisms, such as E. coli, cause disease accidentally, while others, such as Salmonella and Shigella, are always pathogenic to humans and have been reported to have high antibiotic resistance (Nordmann et al. 2011; Payne and Neilands 1988).

Enterobacteriaceae-carbapenem-resistance

Carbapenems, for example, imipenem and meropenem, differ from penicillin because of the broad spectrum of antibacterial activity of a class of β-lactam antibiotics. Carbapenems are used as a last-line treatment for serious infections caused by resistant gram-negative multidrug-resistant bacilli (Paul et al. 2018). Imipenem inhibits transpeptidation by binding strongly to PBP1 and PBP2 and is resistant to many β-lactamases (Nordmann et al. 2012). Imipenem penetrates gram-negative cells well and is also effective against anaerobic bacteria (Moellering Jr et al. 1989). Therefore, it is used therapeutically in the treatment of strains of Acinetobacter, Listeria, Neisseria gonorrheae, Neisseria meningitidis, Pseudomonas aeruginosa, Streptococcus pneumoniae, intestinal gram-negative bacteria and some anaerobic bacteria produced by β-lactams (Kaye and Pogue 2015; Nourbakhsh et al. 2017). In general, carbapenems bind to type 1a, 1b, and 2 PBPs (Fernández-Cuenca et al. 2003). Meropenem has the highest affinity for PBP type 2, followed by 1b and 1a, but it also has a unique affinity for PBP type 3, which is specific for P. aeruginosa (Page et al. 2010). Carbapenem-hydrolyzing enzymes are divided into three distinct groups according to the Ambler classification. The important classes in this group included group A, which included KPC and GES, and group B, which included the New Delhi metallo-β-lactamase (NDM). Group D included various types of OXA (Opazo et al. 2012). The stability of carbapenems against gram-negative pathogens (resistant to other β-lactamases) is due to various factors, such as their protection against AmpC and increased system activity against efflux pumps and broad-spectrum β-lactamases (ESBLSs) (Bush 2015).

Generation of 3rd-generation Enterobacteriaceae cephalosporin-resistant strains

Cephalosporins, such as capsules, syrups, and ampoules, are among the oldest and most abundant antibiotics that affect many pathogens and are produced in various drug forms depending on their generation. Third-generation cephalosporins (affecting gram-negative bacteria) are classified as cefixime, ceftriaxone, ceftazidime, or ceftazidime (intravenous or intramuscular injection). Specifically, first-generation cephalosporins are highly active against S. aureus and Streptococcus species, while their activity against gram-negative bacteria is limited to Proteus mirabilis,

E. coli, and Klebsiella pneumoniae, which can cause pneumonia (Mizrahi et al. 2020). Among gram-negative bacteria, third-generation cephalosporins also cover Serratia species (Hamprecht et al. 2016; Logan et al. 2014). Cephalosporins are more stable than penicillin are many bacterial β-lactamases, so they generally have a wider range of activity. The inherent antimicrobial activity of natural cephalosporins is low, and the binding of different groups, R1 and R2, has produced drugs with good therapeutic effects and few toxic effects (Ehrhardt and Sanders 1993).

Among the types of resistance produced by bacteria, the types that produce the β-lactamase enzyme that is effective against third-generation cephalosporins, especially ceftazidime and cefotaxime, are of particular clinical importance to this group of bacteria, which are called ESBLs (Expanded Spectrum β-Lactamase) (Jones et al. 1997). According to the classification of broad-spectrum enzymes of group A, TEM-1, TEM-2, and SHV-1 are important genes involved in resistance to ampicillin, amoxicillin, and early-generation cephalosporins. CTX-M-type β-lactamases are widely broadcast through ESBLs lacking SHV or TEM. CTX-M was reported in Pseudomonas spp. and Enterobacteriaceae-resistant strains (McGrath and Asmar 2011).

Resistance of acinetobacter baumannii

Acinetobacter baumannii is one of the most important opportunistic pathogens associated with nosocomial infections (Peleg et al. 2008). The excessive use of antimicrobials has led to the emergence of strains with multiple drug resistance patterns that simultaneously resist different classes of antibiotics, including β-lactams, aminoglycosides, and fluocinolone (Karageorgopoulos and Falagas 2008; Nourbakhsh et al. 2018). According to the results, acetyltransferases, acetyltransferases and phosphotransferases play key roles in the development of resistance to aminoglycosides (Ramirez and Tolmasky 2010; Nourbakhsh et al. 2016). Aminoglycoside resistance also occurs because the aacC1 gene encodes an acetyltransferase that can induce gentamicin resistance, similar to the aadA1, aadB and aphA6 genes, which are involved in resistance to streptomycin, the spectinomycin gentamicin, tobramycin and kanamycin, respectively (Akers et al. 2010; Aliakbarzade et al. 2014). Resistance to penicillins and cephalosporins is also common in Acinetobacter strains and can be attributed to the ADC7 and OXAset genes. TEM-1, SCO-1, CARB-4 and OXAs are well known genes that are able to hydrolyze ESBLs, which are the cause of resistance to carbapenems and oxacillin, respectively (Zarrilli et al. 2013).

Helicobacter pylori-resistant

Helicobacter pylori is a gram-negative, curved bacterium without spore flagella. H. pylori is mainly found in the antrum of the human stomach and is permeable through the flagella that allow the bacteria to move (Covacci et al. 1999). According to statistics, the annual incidences of H. pylori infection in developing and developed countries are 4–15% and 0.5%, respectively, which are significant (Gerhard et al. 1999). Concerning the importance of investigating and following this global infection, it is notable that this infectious agent is involved in the occurrence of many common gastrointestinal disorders, including gastritis, duodenal ulcers, peptic ulcers, adenocarcinoma and gastric lymphoma. The antibiotic used in the first-line treatment for H. pylori is metronidazole, which, due to the overuse of this drug in H. pylori infections and other infections, such as parasitic infections, causes the emergence of isolates with high resistance to this antibiotic. A2142G, A2142C, or A2143G gene mutations decrease the affinity for H. pylori treatment drugs to increase drug resistance in strains. Disorders in efflux pumps, ribosomal protein L22 and IF-2 (linked to translation initiation factor 2), have been reported to be effective for H. pylori resistance (Hooi et al. 2017; De Francesco et al. 2010).

Campylobacter resistant

Campylobacter is the most common microorganism involved in food poisoning, with an estimated 2.4 million people visiting the United States each year with symptoms of nausea, heartburn, diarrhea, and fever (Sproston et al. 2018). Campylobacter jejuni and Campylobacter coli are important clinical spp. Resistance to fluoroquinolone antibiotics (such as ciprofloxacin) in Campylobacter bacteria is so high in some countries that these antibiotics are not effective in treating severe cases of the disease (Pope et al. 2007). An amino acid substitution in the gyrase A subunit occurred in the single point mutation C257T. Accordingly, this analysis of gyrA gene expression in Campylobacter spp. revealed other resistance mechanisms of this bacterium, including Cme ABC efflux pump disturbance, cmeR–cmeABC intergenic region mutation and mfd gene mutation (Ajene et al. 2013; Grinnage-Pulley 2013).

Pseudomonas aeruginosa-resistant strains

P. aeruginosa is one of the most important bacteria isolated from different samples of green pus in 1882. The diversity of Pseudomonas infections is due to the expansion of various acquired mechanisms, including the regulation of gene expression (Martin et al. 1991). This bacterium is primarily a nosocomial pathogen and is commonly found in humid hospital environments (Murphy et al. 2008). The most important of these mechanisms include overexpression of the efflux pump, reduced permeability to the outer membrane, or multiple mutations involved in resistance acquisition (Bryan et al. 1972). Resistance to β-lactam antibiotics such as penicillin, cephalosporin and carbapenem has been reported in many studies related to plasmids and is also always due to β-lactamase gene transfer (Giwercman and Høiby 1991). This resistance is mostly due to the production of hydrolyzing enzymes such as metallo-β-lactamases. These enzymes are divided into 4 classes based on their function. Classes A, C and D are operated by the serine mechanism, while class B requires the element zinc for its activity. Class 2 is classified into 8 subgroups: a2, b2, 2be, 2br, c2, 2d, e2, and f2. (Bebrone 2007). According to the results, SHV, TEM, VEB, PER, GES/IBC (class A) and OXA (class D) were detected in Pseudomonas spp. By replacing amino acids in the active site of the SHV enzyme, diverse types of SHV β-lactamases have been identified, and more than 50 SHV enzymes have been identified worldwide. Aminoglycoside-resistant enzymes are also known to be AMEs (Bush and Jacoby 2010). It was reported that aminoglycoside enzymes such as acetyltransferases (AACs), aminoglycoside adenylyl transferase (AADs) and aminoglycoside modifying enzymes (AMEs) impair the ability of antibiotics to bind to infectious agents and thus play a role in bacterial resistance (Kapoor et al. 2017).

Neisseria gonorrheae-resistant strains

Neisseria is one of the most important genera of the genus Neisseria. They are gram-negative (like bean seeds) and immobile diplococcic (Whiley et al. 2018). If the bacteria were resistant to penicillin, ceftriaxone (a third-generation cephalosporin) was used. The sexual partner must also be treated. Antibiotic resistance in gonococci has always been of interest to epidemiologists (Tapsall 2005). In the 1940s, penicillin was identified as an effective antibiotic. In the 1970s, strains resistant to penicillin and tetracycline appeared in Pacific countries. Recently, penicillin-, quinolone- and tetracycline-resistant strains have been reported in some geographical areas. According to reports, penicillinase-producing N. gonorrheae (PPNG) is the most important cause of widespread penicillin resistance in N. gonorrheae. In addition, mutations in genes such as mtrR and changes in genes encoding the DNA enzyme topoisomerase lead to efflux pump dysfunction (MtrC-D-E system) and antibiotic resistance (Tapsall 2005; Unemo and Shafer 2011). Quinolones can induce resistance via mutations in the gene encoding subunit A of the enzyme DNA gyrase (gyrA). Other efflux pump disturbances (NorM pumps) significantly reduce the permeability of the outer membrane to microbial agents (Control and Prevention 2011). The most important pathway is penicillin-binding reduction (Asp-345a incorporation), which induces specific changes in the transpeptidase domain of the penA and penB genes (porin gene) and ultimately the 3rd generation cephalosporin resistance gene (Lindberg et al. 2007).

Haemophilus influenzae resistance

Haemophilus influenza is an important pathogen in the respiratory system that can cause acute middle ear infections, sinusitis, pneumonia and acute bronchitis attacks (Markowitz 1980). Currently, resistance or reduced sensitivity to antibiotics is observed in many strains of this organism. This bacterium is divided into two classifiable groups that have a polysaccharide capsule and an unclassifiable group that does not have a capsule (Cleary et al. 2018). These infections are more common in children and infants and cause complications such as sepsis, meningitis, pneumonia, epiglottis and other unpleasant complications that are more common in serotype b strains (Riley and Cramblett 1981). The genetic diversity of capsule-free strains was greater than that of capsule strains. Strains with serotype b capsules or so-called Hib are the most important disease-causing strains (such as epiglottises). The capsule promotes resistance to phagocytosis and the complement system. Haemophilus influenza is resistant to many antibiotics because it produces β-lactamase enzymes or alters penicillin-binding proteins (Pitout et al. 1997; Ubukata et al. 2001). According to the results, the presence of either TEM-1 or ROB-1 is the most important reason for resistance to ampicillin, which diminishes the affinity of penicillin-binding proteins (Medeiros et al. 1986).

Salmonella spp.-resistant

Salmonella is one of the leading causes of food poisoning. The bacteria involved in this disease can live actively in the body of animals as well as humans (Chalker and Blaser 1988). Salmonella bacteria are found in the intestines of animals such as pigs and poultry and are spread through feces. In terms of serological reactions, nearly 2500 Salmonella serotypes have been identified (Coburn et al. 2007). The most important classification of Salmonella is in the following three categories: Salmonella typhi, Salmonella chlorosis and Salmonella enteritidis (Alban et al. 2002). Fluoroquinolone was identified as an unprecedented antibiotic for Salmonella spp. by the WHO in 2017. These findings explain why FQ-resistant Salmonella strains have been identified (Chiu et al. 2002). Various mechanisms of quinolone resistance have been reported, especially QRDR mutations, which affect gyr and par gene expression and ultimately reduce the affinity of antibiotics for topoisomerase enzymes. On the other hand, plasmid-mediated quinolone resistance (PMQR) directly affects the expression of the Qnr, aac (6’)-lb-cr, oqxAB and qepA genes, which affect efflux pump output and antibiotic resistance (Wong et al. 2014). Recently, resistance to other antibiotics, including chloramphenicol, ampicillin, sulfonamides, streptomycin, and tetracycline, has been reported. The improper use of antibiotics against Salmonella can lead to the emergence of strains that are resistant to even new treatments (Briggs and Fratamico 1999).

Resistance of Shigella spp.

Shigellae are gram-negative, immobile bacilli that are closely related to E. coli and Salmonella. Shigella is pathogenic in humans but not in other animals. It is classified into 4 head groups: Serogroup A (Shigella dysentery), which contains 12 serotypes; Serogroup B (Shigella flexneri), which contains 6 serotypes; Serogroup C (Shigella buidi), which contains 18 serotypes; and Serogroup D (Shigella sonei), which contains 1 serotype. Fluoroquinolone, which is resistant to various mutations in the QRDR region, was reported to be the best treatment for Shigella. According to the results, QRDR region mutations enhance the expression of gyrA,B and parC,E (topoisomerase IV) (Minarini and Darini 2012). Furthermore, plasmid-mediated quinolone resistance due to Qnr genes and efflux pump mediators such as mdfA, tolC, ydhE and marA plays a significant role in Shigella-MDR resistance (Sato et al. 2013).

Plant-derived compounds against gram-negative bacteria

Natural antimicrobial agents are compounds that can stop (bacteriostatic) or kill (bactericidal) microorganism propagation (Nourbakhsh et al.). These antimicrobial agents are classified into various types according to their destructive effects on bacteria, fungi or viruses (Davidson et al. 2012). The toxicity of these compounds to humans and other animals is negligible. In recent years, the importance of biofilms in causing disease, the spread of microbial resistance, and the side effects of antibiotics have led researchers to use natural compounds to obtain new antimicrobial agents. Natural products are the best candidates for controlling antibiotic-resistant infections, the advantages of which include low production costs and few side effects. Medicinal plants, which contain many secondary metabolites, are the active ingredients of many drugs. As a result, these plants can be considered one of the most important sources of drugs with new antimicrobial effects. In the following, we will discuss some of these natural compounds with antimicrobial activities against gram-negative bacteria.

Phenolic compounds

Biochanin A

Biochanin-A (BCA, 1), an O-methylated isoflavone, is detectable in legume plants, cabbage and alfalfa and has antibacterial, antioxidant, anti-inflammatory and antiparasitic properties (L. chagasi amastigotes) (Raheja et al. 2018; Arjunan et al. 2018). Because of these properties, the antibacterial activity of BCA has been investigated in various studies. BCA, with an IC₅₀ of 12.0 µM, was determined to be an efflux pump activity enhancer (Hanski et al. 2014). It is able to reduce the MIC in Chlamydia trachomatis-resistant strain-infected HeLa cell cultures with an IC₅₀ value of 6.5 µM (Pohjala et al. 2012). Although the mechanism of action of BCA remains unknown, the protective effects of BCA on Enterobacteriaceae infections were reported in Meng-Ying He studies (He et al. 2014). These authors demonstrated that BCA disrupted the cell membrane of the E. coli ATCC25922 strain (MIC90 > 10,000 µg/mL), which can be preferable to other flavonoids. In agreement with these findings, He et al. demonstrated that BCA is able to disrupt the membrane of E. coli ATCC 25922 by altering fluidity and integrity (He et al. 2014). In relation to other members of the Enterobacteriaceae family, the protective effects of BCA (0.84–1.69 mg/cm³) on K. pneumoniae infections and P. aeruginosa (0.84 mg/cm³) have been reported (Nikolic et al. 2018).

Kaempferol

Various beneficial effects of kaempferol (2), especially its antioxidant, anti-inflammatory, anticancer and antimicrobial properties, have been reported in different studies (Ren et al. 2019). Furthermore, it is also able to disrupt the bacterial cell membrane (Vikram et al. 2010). Kataoka et al. demonstrated that 2 mg/kg daily consumption of kaempferol for 7 days has antimicrobial activity against H. pylori (Kataoka et al. 2001). Moreover, kaempferol significantly inhibited H. pylori growth in a dose-dependent manner (Escandón et al. 2016). The number of Klebsiella-infected mice decreased during daily administration of kaempferol for 7 days. Teffo et al. (Teffo et al. 2010) also indicated that kaempferol has good antimicrobial properties against P. aeruginosa and E. coli ATCC25922, with MIC values of 63.0 µg/mL and 16.0 µg/mL, respectively. Additionally, the glycosylated form of 2 showed significant activity against E. coli (MIC = 2.0 μg/ml), K. pneumoniae (MIC = 4.0 μg/ml), and A. baumannii (MIC = 8.0 μg/ml) (Özçelik et al. 2006). Similar results were observed in another study in which seven kaempferol rhamnoside derivatives showed strong activity against P. aeruginosa (MIC range of 1–128 μg/ml) and S. typhi (MIC range of 1–64 μg/ml) (Tatsimo et al. 2012). Kaempferol in combination with colistin had a strong synergistic effect on colistin-resistant gram-negative bacteria, including P. aeruginosa (MIC range 0.03–0.26 μg/ml), A. baumannii (MIC range 0.12–0.51 μg/ml), E. coli (MIC range 0.01–0.37 μg/ml), and K. pneumoniae (MIC range 0.04–0.75 μg/ml). The authors suggested that bacterial membrane lysis may be the mechanism of action of the observed activity (Zhou et al. 2022).

Quercetin

Quercetin (3) is a flavonol that is present in most fruits, vegetables, leaves and seeds. It can also be used in supplements, wines, or foods (Lakhanpal and Rai 2007). Wu et al. (Wu et al. 2008) reported that quercetin has inhibitory effects on H. pylori at an MIC of 100 μg/ml. Quercetin can target D-alanine: D-alanine ligase to induce antimicrobial effects (Wu et al. 2008). A recent study by Pal et al. revealed that quercetin had a lower MIC (16–256 μg/ml) than meropenem against carbapenem-resistant Enterobacteriaceae. Quercetin in combination with meropenem exhibited even better antibacterial activity against E. coli and K. pneumoniae (Pal and Tripathi 2020). Quercetin was reported to exert such activity by disrupting biofilm formation and the integrity of the cell wall and cell membrane. The results in animal samples also indicated the reduction effects of the oral administration of quercetin (20 mg) and vitamin C (500 mg) in K. pneumoniae- and P. aeruginosa-infected rats. Of course, the results indicate bacteriostatic activity and a reduction in the number of bacteria counted (Waad et al. 2020). In addition, an in vivo study demonstrated that quercetin at a dosage of 200 mg/kg bw/day decreased H. pylori infection in the gastric mucosa and reduced both the inflammatory response and lipid peroxidation (González-Segovia et al. 2008). Inhibition of nucleic acid synthesis and disruption of the plasma membrane were reported as the modes of action of quercetine against E. coli, P. aeruginosa, and S. typhimurium (Yang et al. 2020).

Epigallocatechin gallate

Epigallocatechin gallate (EGCG, (4)) is found in vegetables, nuts, tea and even fruits. EGCG prevents the growth of cancer cells without affecting healthy cells (Li et al. 2023). Destructive effects of EGCG against gram-negative bacteria have been identified in various studies (Mittal et al. 2020). The authors indicated that EGCG has strong antibiotic activity against 18 isolates of gram-negative Stenotrophomonas maltophilia strains (MIC = 4–256 μg/ml). It was also reported that EGCG has inhibitory activity against dihydrofolate reductase, which is an important target for the expansion of antibacterial agents (Navarro-Martínez et al. 2005). EGCG is also able to have antibacterial activity against E. coli by inhibiting β-ketoacyl-[acyl carrier protein] reductase, increasing FabG aggregation and inactivation (Li et al. 2006). These outcomes suggest that various chemical reactions necessary for inactivation occurred during the lag time (Li et al. 2006). In another study, EGCG exhibited activity against ten strains of P. aeruginosa with an MIC range of 200–400 µg/ml, while it displayed an MIC of 400 µg/mL against 10 strains of E. coli. (Jeon et al. 2014) In 2022, an MIC of 160 µg/ml was obtained for EGCG against another gram-negative bacterium, Shewanella putrefaciens ATCC 8071, through the damaging effect of the bacterial cell wall and membrane (Pei et al. 2022). In a study by Siriphap et al., the effect of EGCG on 45 MDR Vibrio cholerae clinical isolates was evaluated. The MIC ranged from 62.5 to 250 µg/ml. Moreover, the combination of EGCG and an antibiotic (tetracycline) showed better activity than treatment alone (Siriphap et al. 2022). Furthermore, the authors concluded that EGCG has significant antibacterial effects on K. pneumoniae, P. mirabilis, P. aeruginosa, Serratia marcescens and S. typhi, which are important gram-negative rods (Yoda et al. 2004). EGCG is able to bind to bacterial porins, affects porin pores and disrupts outer membrane permeability (Li et al. 2006). The results of earlier studies indicated that EGCG is able to target the passive transport of small hydrophilic molecules, such as glucose uptake by the E. coli cell membrane (Nakayama et al. 2013). The synergistic bactericidal effect of EGCG (18 h treatment) with paraquat was also reported by Xiong et al. It was reported that EGCG treatment for 18 h had a 46.5% efficiency at 100–1000 μM (Xiong et al. 2017). The antibacterial susceptibility of A. baumannii to EGCG was investigated by Betts et al., who reported MICs of 128–1024 μg/ml against multidrug-resistant strains. They also reported that curcumin has synergistic effects with EGCG (MIC > 256 μg/ml), and time-kill curves were generated for curcumin-EGCG (1:8 and 1:4) (Betts and Wareham 2014). Very recently, Zhang et al. reported an EGCG MIC of 400 μg/ml against Shigella flexneri. They proposed that the production of hydroxyl radicals, which promote oxidative damage to cell membranes and destroy cell membrane integrity, may contribute to the antibacterial activity of EGCG against S. flexneri (Zhang et al. 2023).

Apigenin

As a flavone, apigenin (5) displayed moderate antibacterial activity against H. pylori (MIC = 25 μg/ml) (Wu et al. 2008). In another study, a series of synthetic apigenin derivatives were shown to have broad-spectrum antibacterial activity (MIC = 3.6–62.5 μg/ml) against two gram-negative bacteria, E. coli and P. aeruginosa (Liu et al. 2013). Kim et al. reported the potent inhibitory activity of apigenin toward E. coli, with an MIC of 2.5 μg/ml, through the induction of apoptosis‐like death triggered by the production of reactive oxygen species (ROS)/reactive nitrogen species (RNS), primarily nitric oxide (NO) and O²⁻ (Kim et al. 2020). Basile et al. tested apigenin against several gram-negative and gram-positive bacteria (Basile et al. 1999). The MICs ranged from 4 to 128 μg/ml against E. cloacae, E. aerogenes, P. aeruginosa, E. coli, S. typhii, K. pneumonia, and P. mirabilis. Interestingly, apigenin-7-O-triglucoside had lower activity (256 μg/ml) than apigenin against the abovementioned gram-negative bacteria. Other studies have also reported that the decrease in the antimicrobial activity of flavonoids caused by glycosylation may be due to a reduction in antibacterial power due to a reduction in the hydrophobicity of flavonoids (Fang et al. 2016). In 2013, Eumkeb and Chukrathok (Eumkeb and Chukrathok 2013) evaluated the antibacterial properties of apigenin and naringenin in combination with ceftazidime against ceftazidime-resistant Enterobacter cloacae (CREC). They revealed the synergistic effect of both flavonoids (3 μg/ml) and ceftazidime (3 μg/ml) on reversing bacterial resistance to this cephalosporin against CREC. These authors suggested that the activity of apigenin could possibly occur through the inhibition of peptidoglycan synthesis, suppression of certain-lactamase enzymes and alteration of the outer membrane (OM) and the permeabilization of the cytoplasmic membrane (CM). In addition, a preliminary structure–activity relationship (SAR) study showed that the presence of three hydroxyl groups at the 5, 7, and 4' positions in apigenin and naringenin is necessary for synergistic activity. Kuo et al. (2014) showed that apigenin (60 mg/kg bw/day) significantly decreased H. pylori-induced inflammation and atrophic gastritis in Mongolian gerbils by inhibiting the activation of NF-κB and the antioxidant activity of apigenin.

Sakuranetin

Sakuranetin (6), a flavone, is widely found in rice, Polyomnia fruticosa, grass trees, shrubs, cheery plants, flowering plants, and glycosides (sakuranin). The anticancer activity of 6, especially against esophageal squamous cell carcinoma (ESCC), melanoma and colon cancer (Colo 320), has been reported in various studies (Stompor 2020). Antiprotozoal, antibacterial, antiviral (against human rhinovirus 3 and influenza B) and anti-inflammatory activities of 6 have been reported in several studies (Stompor 2020). Zhang et al. in 2008, reported that anti-H. pylori activities of three natural flavonoids, quercetin (MIC of 330.9 μM), apigenin (MIC of 92.5 μM), and sakuranetin (MIC of 87.3 μM). They demonstrated that the mentioned flavonoids exerted their anti-H. pylori activities through the inhibition of enzymes related to fatty acid biosynthesis (Fab), such as FabG, FabI and FabZ, which leads to their aggregation and ultimately bacterial cell death. Sakuranetin (6) inhibited the H. pylori FabZ enzyme (HpFabZ) with an IC₅₀ of 2.0 μM, which was much greater than that of quercetin (39.3 μM) and apigenin (11.0 μM). From the SAR point of view, the presence of a methoxy group at position C-7 may be vital for increasing the inhibitory activity (Zhang et al. 2008).

Curcumin

Curcumin (7), a natural phenolic compound, has numerous biological activities, such as antioxidant, antimicrobial, anticancer, anti-inflammatory, and hepatoprotective effects (Li et al. 2021). Due to the medicinal properties of curcumin, especially its antimicrobial effects, we refer to various studies on the effects of curcumin on gram-negative bacteria.

Very recently, Tamfu et al. (Tamfu et al. 2020) investigated the antimicrobial activity of Camellia sinensis and Curcuma longa extracts. These authors reported that C. longa (MIC = 312.5 µg/ml) had better activity against P. aeruginosa than C. sinensis (MIC = 625 µg/ml). Oral administration of curcumin (200 mg/kg) alone or especially combined with antibiotics (metronidazole, 8 μg/g; erythromycin, 16 µg/g; bismuth substrate, 8 µg/g) significantly inhibited H. pylori infections, as evidenced by reductions in gastrin, IFN-γ, and MPO activity and lipid peroxidation (Ranjbar and Mohammadi 2018). In another in vivo study, curcumin (200 mg/kg) reduced nuclear factor (NF)-κB p65 expression in the gastric mucosa of H. pylori-infected rats (Sintara et al. 2010). In vivo studies of the antibacterial effects of curcumin on H. pylori compared with those of other drugs, especially metronidazole and omeprazole, confirmed that chemical drug treatment has poor activity (5.9–78.9%). In addition, inflammatory cytokine secretion was reduced due to treatment with curcumin in H. pylori-infected patients (Koosirirat et al. 2010). This finding is consistent with the in vivo results indicating that, compared with one week of treatment with lactoferrin, pantoprazole or N-acetylcysteine, curcumin therapy reduces the immunological risk of gastric inflammation and dyspeptic symptoms (Di Mario et al. 2007). Various studies, especially in vivo studies in H. pylori-infected C57BL/6 mice, confirmed the ability of curcumin to eradicate gastric damage (De et al. 2009).

Recently, a solid dispersion containing curcumin and an octenylsuccinate hydroxypropyl phytoglycogen was shown to have better antibacterial activity against three strains of H. pylori (MBC = 20 μg/ml). Furthermore, curcumin medicated with silver nanocomposites exhibited stronger antibacterial activity against E. coli. In addition, sodium carboxymethyl cellulose silver nanocomposite films (SCMC SNCFs) loaded with curcumin have efficient antibacterial properties (Varaprasad et al. 2011). Curcumin-encapsulated chitosan silver nanocomposite films exhibit synergistic effects against E. coli in wound dressings (Vimala et al. 2011). In some other studies, curcumin had variable anti-H. pylori effects, with an MBC ranging from 5 to 50 μg/ml against 65 clinical isolates of H. pylori (De et al. 2009) and an MBC ranging from 25 to 50 μg/ml against H. pylori isolated in Pakistan and Japan (Zaidi et al. 2009).

In terms of food safety, the authors indicated that the addition of 0.3% (w/v) curcumin extract could reduce the bacterial count, especially for P. aeruginosa, S. typhimurium and E. coli 0157:H7 (Hosny et al. 2011). In our previous paper, we reviewed the antibacterial potential of several metal complexes of curcumin. For example, the complexation of curcumin with zinc, nickel, cobalt and copper increased the activity against P. aeruginosa and E. coli (MIC range, 11.2–12.9 μg/ml) (Chandrasekar et al. 2014; Shakeri et al. 2019). Very recently, Gholami et al. revealed a much greater MIC of metallo-complexes (Cu, Zn, and Fe) of curcumin (MIC of 62.5 µg/ml) than of curcumin alone (MIC of 125 µg/ml) against P. aeruginosa PAO1 (Gholami et al. 2020). Other researchers have introduced indium curcumin, diacetyl curcumin and indium diacetyl curcumin as antibacterial complexes of curcumin. An in vitro study indicated that indium curcumin and indium diacetyl curcumin have significant antibiotic susceptibility effects on E. coli (MIC of 93.8 μg/ml) and P. aeruginosa (MIC of 23.4 μg/ml) (Tajbakhsh et al. 2008). According to the results, curcumin with cobalt nanoparticles showed high antibacterial activity against E. coli strains (Hatamie et al. 2012).

Eugenol

The most important sources of eugenol (8) include nutmeg, clove oil, cinnamon and basil. It is yellow in color and is present at a concentration of 82–88% in clove leaf oil (Chaieb et al. 2007). Ma et al. reported the MIC of 133 μg/ml of eugenol against Legionella pneumophila, a gram-negative bacterium, via its disruptive effect on the bacterial cell envelope (Jiangwei et al. 2017). It was demonstrated that eugenol has effective properties in addition to being a MRSA biofilm producer (Yadav et al. 2015; Kyaw and Lim 2012). Furthermore, eugenol was observed to damage the cell membrane and biofilm production and cause leakage of the cell contents (Yadav et al. 2015). The antibacterial effect of eugenol was evaluated against E. coli, E. aerogenes and P. aeruginosa by disrupting cell membrane production. Yadav et al. also reported that eugenol reduces the expression of genes related to biofilm and enterotoxin production (Yadav et al. 2015). Rathinam et al. also indicated that eugenol exhibited equivalent effects on the biofilm structure and virulence feature synthesis of P. aeruginosa (Rathinam et al. 2017).

Cinnamaldehyde

Cinnamaldehyde (9), a phenylpropanoid, is used as a flavoring and odor agent in cinnamon in the food and perfume industries. It also makes up more than half of the ingredients in cinnamon bark (55–76%) and was isolated from cinnamon essential oil (EO) in 1834 (Didry et al. 1994). Cinnamaldehyde showed promising antibacterial activity against E. coli and K. pneumoniae (MIC of 62.5 μg/ml) and against Proteus mirabilis and P. aeruginosa (MIC of 125.0 μg/ml) (Al-Bayati and Mohammed 2009). In another study by Ooi et al. (2006) cinnamaldehyde exhibited broad-spectrum antibacterial activity against several gram-negative bacteria, including E. coli and P. aeruginosa (MIC of 300 μg/ml), the genus Enterobacter (MIC of 250 μg/ml), Vibrio cholera (MIC of 150 μg/ml), V. parahaemolyticus (MIC of 75 μg/ml), S. typhimurium and P. vulgaris (MIC of 150 μg/ml). Moreover, cinnamaldehyde displayed strong activity against L. pneumophila, with an MIC of 15–31 μg/ml and an MBC of 31–62 μg/ml (Jiangwei et al. 2017). In another study, a cinnamaldehyde MIC of 3 mM was observed against E. coli (Malheiro et al. 2019). Moreover, cinnamaldehyde showed activity against multidrug-resistant E. coli (MIC = 157 μg/ml) and multidrug-resistant P. aeruginosa (MIC = 630 μg/ml) (Sim et al. 2019). Yin et al. in 2020, showed that the MIC and MBC of cinnamaldehyde against drug-resistant Aeromonas hydrophila were 256 and 512 μg/ml, respectively. They concluded that cinnamaldehyde kills gram-negative bacteria by disrupting the cell membrane and affecting protein metabolism (Yin et al. 2020). Shen et al. evaluated the anti-E. coli mechanism of cinnamaldehyde in their study. The authors indicated that under the MIC of cinnamaldehyde (0.31 mg/mL), bacterial cell permeability, cell membrane integrity and bacterial cell morphology were impaired (Shen et al. 2015). In addition, He et al. demonstrated that cinnamaldehyde exerted its anti-E. coli activity by increasing the permeability and oxidizing the cell membrane (He et al. 2019). Topa et al. reported that cinnamaldehyde has potent anti-P. aeruginosa activity, with an MIC of 11.8 mM. They revealed that swarming motility and biofilm production in P. aeruginosa are specifically stopped by cinnamaldehyde, which easily disrupts the membrane of this organism (Topa et al. 2018). In a major advance, the authors also reported that cinnamaldehyde has a specific mechanism against E. coli strains, which was confirmed by scanning electron microscopy. This evidence also highlights that the bacterial cell membrane is also damaged in the presence of EOs (Zhang et al. 2015).

Coumarins

Coumarins are a significant class of natural products that consist of fused benzene and α-pyrone rings. Coumarins exhibit a broad range of antimicrobial activities. Novobiocin and Chlorobiocin are two of the best examples of antimicrobial compounds with a coumarin skeleton (Al-Majedy et al. 2017). However, from a literature survey, it was found that most naturally occurring coumarins have better antibacterial activity against gram-positive bacteria. For example, in a study, a series of 45 coumarin derivatives were tested for their antibacterial activity against a wide variety of gram-positive and gram-negative bacteria, such as E. coli and P. aeruginosa. The results indicated that all the compounds showed weak activity against gram-negative bacteria (MIC = 250–2000 μg/ml) (de Souza et al. 2005). In another study, the anti-QS and antibiofilm activities of coumarins against three gram-negative bacteria, Chromobacterium violaceum 12,472, Serratia marcescens MTCC 97, and P. aeruginosa PAO1, were reported through the inhibition of acylhomoserine lactone synthases, the antagonization of QS-regulatory proteins, and the blocking of receptor proteins (Qais et al. 2021).

Aegelinol and agasyllin

Aegelinol (10) and agasyllin (11), two pyranocoumarins, are found in Ferulago asparagifolia, Aegle marmelos and the roots of Ferulago campestris. Both compounds have antibacterial effects on gram-negative bacteria, especially S. typhii (MICs of 16 and 32 μg/ml), E. aerogenes (MICs of 16 and 32 μg/ml) and E. cloacae (MICs of 16 and 32 μg/ml, respectively). These compounds also exhibited dose-dependent antibacterial activity against H. pylori strains (5–25 μg/ml). The reported antimicrobial mechanism of this compound includes DNA gyrase inhibition (Basile et al. 2009).

Asphodelin A

Asphodelin A (12), an aryl coumarin, is extracted from the bulbs and roots of Asphodelus microcarpus. Compound 12 has potent antibacterial activity against E. coli and P. aeruginosa (MIC = 4 and 8 μg/ml, respectively). However, its glycosylated derivative, asphodelin A 4′-O-β-D-glucoside, had only moderate activity (MIC = 128 and 256 μg/ml, respectively) (El-Seedi 2007). The chemical structures of the phenolic compounds are shown in Fig. 2.

Fig. 2

Chemical structures of phenolic compounds

Terpenoids

Monoterpenes

Carvacrol/thymol

Carvacrol (13) is a powerful antimicrobial compound that kills harmful and pathogenic bacteria by increasing the permeability of the bacterial cell membrane, disrupting the ionic balance on both sides of the membrane, and ultimately leading to destruction of the bacterial cell membrane (Sharifi‐Rad et al. 2018; Marinelli et al. 2018). Because of their strong antifungal activity, Abbaszadeh et al. also suggested thymol (14) and carvacrol in addition to eugenol and menthol as good alternatives to synthetic fungicides in the food industry (Tominaga et al. 2002). In addition, five thymol derivatives, 8,9,10-trihydroxythymol (15), thymol-β-glucopyranoside (16), 9-hydroxythymol (17), 8,10-dihydroxy-9-isobutyryloxythymol (18), and 8-hydroxy-9,10-diisobutyryloxythymol (19), which were isolated from Centipeda minima, showed antibacterial effects on S. typhimurium, with MIC values of 6.25, 25, 50 and 25 μg/ml, respectively (Liang et al. 2007). Carvacrol can also inhibit cell membrane disturbance and efflux pump mechanisms (Sridevi et al. 2017). The antibacterial properties of thymol and carvacrol were confirmed by Althunibat et al. against E. coli, E. aerogenes and P. aeruginosa (MIC = 5–8 µg/mL) (Althunibat et al. 2016). More details can be found in another study that indicated that carvacrol has antibiofilm properties against Salmonella spp. (S. typhimurium, S. enteritidis and S. saintpaul). The results demonstrated that there was great inhibition of growth on all tested bacterial isolates except P. aeruginosa (Bnyan et al. 2014). The antibacterial properties of carvacrol and thymol ranged from 200 to 1600 μg/ml and 62–250 μg/ml, respectively, and the antibiofilm effects ranged from 125 to 500 μg/ml and 400–1600 μg/ml, respectively. More recent evidence highlights that Seoul imipenemase (SIM) shows the highest sensitivity in carvacrol-treated isolates, which is in contrast to NDM (New Delhi metallo-β-lactamase). In a major advance in 2017, Raei et al. reported that carvacrol and thymol have protective effects against carbapenemase-producing gram-negative bacterial infections. In another study by Pourhosseini et al., it was found that carvacrol-rich EOs of Z. multiflora had MICs of 0.03–1.0 mg/mL against E. coli (Pourhosseini et al. 2020). These findings support the use of natural compounds as candidates for gram-negative resistant bacteria. Additionally, the antibiofilm effects of carvacrol confirmed that it is able to inhibit biofilm configuration in carbapenemase-producing strains (Raei et al. 2017). The chemical structures of the terpenoids are shown in Fig. 3.

Fig. 3

Chemical structures of terpenoids

Diterpenoids

Several diterpenoids have shown some degree of antibacterial activity against some gram-negative bacterial strains. 3α-Hydroxy-ent-kaur-16-en-19-oic acid (20), ent-kaur-16-en-19- oic acid (21) and 3α-cinnamoyloxy-ent-kaur-16-en19-oic acid (22), three ent-kaurane diterpenoids obtained from Wedelia trilobata, exhibited potent activity against S. dysenteriae (MIC = 3.125–12.5 μg/ml) (Ren et al. 2015). Plectranthroyleanone A (23), an abietane diterpenoid isolated from Plectranthus africanus, displayed activity against P. aeruginosa and K. pneumoniae with MIC values of 150 µg/mL, while plectranthroyleanones B (24) and C (25) showed better activity toward K. pneumoniae (MIC = 37.5 µg/ml) (Nzogong et al. 2018b). Ferruginol (26) and isopimaric acid (27), two diterpenoids from Cryptomeria japonica, showed moderate antibacterial activity toward E. coli (MIC = 50 µg/ml) (Cheng and Chang 2014). In another study, turraeanin G (28), a labdane diterpenoid from Turraeanthus africanus, showed strong activity against E. coli with an MIC of 10 µg/ml (Chenda et al. 2014). Moreover, two serrulatane diterpenoids, 8,19-dihydroxyserrulat-14-ene (29) and 8-hydroxyserrulat-14-en-19-oic acid (30), from Eremophila neglecta, displayed potent activity against Moraxella catarrhalis with MICs of 3.1 and 6.2 µg/ml, respectively (Anakok et al. 2012). Seven isopimarane diterpenoids (31–37) derived from the alga Rhizoclonium hieroglyphicum have shown significant activity against four gram-negative bacteria, E. coli, P. aeruginosa, K. pneumoniae and P. mirabilis, with MICs ranging from 9.0 to 19 μg/ml (Perez Gutierrez and Garcia Baez 2011). Hativene A-C (38–40), lupulin A (41) and 14,15-dihydroajugapitin (42), five diterpenoids isolated from Ajuga pseudoiva, had potent activity against E. coli, P. aeruginosa and S. typhimurium, with MIC values ranging between 15 and 35 µg/ml (Ben Jannet et al. 2006). Murthy et al. investigated the antibacterial activity of two clerodane diterpenoids (16α-hydroxy-cleroda-3,13(14)Z-diene-15,16-olide (43)) and 16-oxo-cleroda-3,13(14)E-diene-15 oic acid (44) from Polyalthia longifolia against a panel of gram-negative bacteria. All tested compounds showed substantial activity against E. coli (MIC = 0.78 and 1.56 µg/ml), Klebsiella aerogenes (MIC = 1.56 and 1.56 µg/ml), P. aeruginosa (MIC = 0.78 and 3.1 µg/ml), P. putida (MIC = 3.1 and 3.1 µg/ml), S. typhimurium (MIC = 0.78 and 1.5 µg/ml), Sarcina lutea (MIC = 1.5 and 3.1 µg/ml), and Nocardia sp. (MIC = 3.1 and 6.2 µg/ml). Notably, the MIC ranged from 3.1 to 6.2 μg/ml for the positive control gentamycin (Marthanda Murthy et al. 2005). The chemical structures of the diterpenoids are shown in Fig. 4.

Fig. 4

Chemical structures of diterpenoids

Triterpenes

A number of studies have demonstrated the promising antimicrobial properties of triterpenoids (Nzogong et al. 2018a; Mbougnia et al. 2020). Isopseudolarifurocic acid A (45), obtained from Pseudolarix kaempferi, exhibited potent activity toward E. coli with an MIC of 0.1 mM (Yang and Yue 2001). Shai et al. reported the broad-spectrum antibacterial activity of four triterpenoids isolated from Curtisia dentata against two gram-negative bacteria, E. coli and P. aeruginosa: lupeol (46) (MIC = 250 and 250 μg/ml), betulinic acid (47) (MIC = 250 μg/ml), ursolic acid (48) (MIC = 250 and 4.0 μg/ml), and 2α-hydroxyursolic acid (49) (MIC = 250 and 7.8 μg/ml) (Shai et al. 2008). In another study by Hu et al., tirucallane-type triterpenoids (50–56) and limonoids (57–58) isolated from Dysoxylum lukii exhibited moderate activity, with MICs ranging from 15.2 to 24.23 μg/ml against three gram-negative bacteria, namely, E. coli, E. cloacae, K. pneumoniae and P. aeruginosa (Hu et al. 2012). Four triterpenoids (dysoxylumin B (59), 24-nor-5α,13-α,14-α,17-α-chola-7,20,22-trien-3-one (60), dysoxylumin C (61) and 24-norchola-1,20,22-triene-3,7-dione (62)) isolated from Dysoxylum densiflorum displayed significant antibacterial activity against five gram-negative bacteria, E. coli (MIC range, 1.6–2.6 μM), E. cloacae (MIC range, 1.0–2.8 μM), K. pneumoniae (MIC range, 1.2–2.9 μM), P. aeruginosa (MIC range, 1.7–2.9 μM), and S. dysenteriae (MIC range, 1.4–2.9 μM) (Hu et al. 2014b). In another study by Wang et al., several oleanane-type triterpenoids (63–75) were isolated from Akebia trifoliata. The isolated compounds showed strong to weak antibacterial activity against three gram-negative strains, E. coli, S. enterica and Shigella dysenteriae, with MICs ranging from 3.9 −  > 125 μg/ml (Wang et al. 2015). Very recently, the triterpene 2-hydroxydiplopterol (76) isolated from soil fungus Aspergillus ochraceopetaliformis showed moderate activity against E. coli (MIC of 470 μg/ml), E. cloacae (MIC of 650 μg/ml), K. pneumoniae (MIC of 610 μg/ml), and P. aeruginosa (MIC of 520 μg/ml) (Asmaey et al. 2021). Three pentacyclic triterpenoids (77–79) isolated from Ilex hainanensis exhibited moderate activity against Fusobacterium nucleatum, with MICs ranging from 79.1 to 156.3 μg/ml (Zhao et al. 2019). Betulinic acid-3-trans-caffeate (80), a triterpenoid from Acacia ataxacantha, showed moderate activity against P. aeruginosa (MIC and MBC of 25 μg/ml) (Amoussa et al. 2016). Additionally, α-amyrenol (81), a triterpene isolated from A. ataxacantha, displayed better activity (MIC = 12 μg/ml) against E. coli and S. typhi. (Aba et al. 2015) Two other triterpenoids, 2α-hydroxy-3-oxolup-12(13), 20(29)-dien-27,28-dioic acid (82) and 2α, 27-dihydroxyphenyl-3-oxo-lup-12(13), 20(29)-dien-28-oic acid (83), extracted from Malus domestica, exhibited good activity toward E. coli (MIC = 37 and 18 μg/ml, respectively) and P. aerinosaose (MIC = 29 μg/ml, for both cases) (Selim and Litinas 2015). In a major advance in 2015, Broniatowski et al. investigated two pentacyclic triterpenes (α-amylin (84) and ursolic acid (85)) with antibacterial properties. They confirmed this activity by the interaction of the two compounds with the inner cell membrane of E. coli and concluded that these compounds are able to disrupt the bacterial outer membrane (Broniatowski et al. 2015). In addition, ursolic acid presented antibacterial activity against carbapenem-resistant K. pneumoniae, which was confirmed by the agar dilution method. The cell membrane potential was also confirmed by the influence of ursolic acid on bacterial cell architecture (Qian et al. 2020). Antimicrobial susceptibility to P. aeruginosa indicated that ursolic acid has antibacterial and antibiofilm activity in liquid suspension cultures (planktonic cells). These results indicate that ursolic acid may be useful when it is administered in combination with β-lactam antibiotics to combat bacterial infections caused by some gram-positive pathogens (Kurek et al. 2012). Biofilm formation in E. coli, P. aeruginosa, V. harveyi and hepatocytes was inhibited by 10 μg/ml ursolic acid (Ren et al. 2005). The chemical structures of the triterpenoids are shown in Fig. 5.

Fig. 5

Chemical structures of triterpenoids

Alkaloids

Several alkaloids have been reported to be potent antimicrobial agents. Two tetrahydrobisbenzylisoquinoline alkaloids, namely, tetrandrine (86) and limacusine (87), which were isolated from Phaeanthus ophthalmicus, strongly inhibited the growth of the gram-negative MDR bacteria MβL-Pseudomonas aeruginosa and Klebsiella pneumoniae + CRE, with an MIC of 68.7 μg/ml for both strains. It was suggested that the presence of rigid aromatic rings and centrally locked nitrogen atoms in both compounds is essential for the observed antibacterial activity (Magpantay et al. 2021). In another study, opuntisine A (88), a cyclopeptide alkaloid of Opuntia stricta, exhibited activity against E. coli with an MIC of 66.7 µg/mL (Surup et al. 2021). Berberine (89), a plant-derived isoquinoline alkaloid, has been reported to be an antimicrobial agent (Budeyri Gokgoz et al. 2017). Berberine binds and inhibits the cell division protein FtsZ and decreases the number of Z-rings in E. coli (Boberek et al. 2010). Berberine also significantly inhibited biofilm formation and quorum sensing in P. aeruginosa PA01 at concentrations ranging from 19 to 1250 µg/mL (Aswathanarayan and Vittal 2018). However, several authors have reported the weak antimicrobial activity of berberine, especially against gram-negative bacteria. In addition, the efflux of berberine by MDR pumps is one of the main problems for its clinical use (Budeyri Gokgoz et al. 2017). To circumvent this drawback, the combination of berberine with other antibiotics is a promising approach. For instance, berberine (80 μg/ml) in combination with tobramycin showed a twofold increase in inhibitory activity (MIC =  < 0.12–64 μg/ml) against MexXY-OprM (the most important mechanism of extrusion of antimicrobial agents in P. aeruginosa strains) compared to that of tobramycin alone (MIC = 0.12- > 128 μg/ml) toward 30 tested P. aeruginosa clinical isolates (Laudadio et al. 2019). Very recently, while berberine and azithromycin alone showed weak activity against P. aeruginosa with MICs of > 1250.0 and 256.0 μg/ml, respectively, a combination of both displayed notable effects (MICs = 312.5–64.0 μg/ml), and a significant reduction in biofilm formation, as evidenced by a reduction in alginate production by P. aeruginosa, was observed (Zhao et al. 2022). In agreement with our findings, lower MICs were obtained with the combination of berberine and imipenem (zero to twofold, MIC = 1.0–16.0 μg/ml) and berberine and ciprofloxacin (zero to onefold, MIC = 2.0–16.0 μg/ml) (Mahmoudi et al. 2020). Similar results were observed for the combination of berberine and ciprofloxacin in ciprofloxacin-resistant isolates of P. aeruginosa (Aghayan et al. 2017). Therefore, the use of berberine as an antibiofilm and quorum sensing inhibitor agent could be used as an auxiliary treatment to increase the effect of antibiotics. A novel alkaloid, chamaedrone (90), was isolated from the roots of Melochia chamaedrys (Sterculiaceae) and was found to be active against S. setubal, E. coli, K. pneumoniae and P. aeruginosa, with MICs of 50, 12.5, 50 and 50 µg/mL, respectively (Dias et al. 2007). In another study by Hu et al., 8-acetylnorchelerythrine (91) was extracted from the roots of Toddalia asiatica. This compound exhibited activity against E. coli, E. cloacae, P. aeruginosa, K. pneumoniae and S. dysenteriae with MIC values of 110, 150, 130, 120 and 120 µg/mL, respectively (Hu et al. 2014a). Buphanidrine (92) and distichamine (93) were identified as new crinane alkaloids from the ethanolic extract of bulbs of Boophone disticha. Both MICs were against E. coli and K. pneumoniae (Cheesman et al. 2012). Chromatographic separation of the chloroform extract of the bark of Artabotrys crassifolius resulted in the isolation of alkaloids such as artabotrine (94), liridine (95), and lysicamine (96). These compounds were found to be active against the gram-negative bacteria extended-spectrum β-lactamase-producing K. pneumoniae (ESBL-KP), with MIC values of 2.5, 2.5 and 10 µg/mL, respectively (Tan et al. 2015). Based on the results of another study, Cinchona alkaloids from the bark of the Cinchona tree, namely, cinchonine (CN) (97) and cinchonidine (CD) (98), displayed activity against E. coli, K. pneumoniae, and P. aeruginosa, with MICs of 25, 100, and 125 µg/mL for CD and 25, 50 and 12.5 µg/mL for CN, respectively (Ramić et al. 2021). Three novel crinane-type alkaloids, crinumlatines A-C (99–101), were isolated from the bulbs of Crinum latifolium. The authors indicated that these compounds presented various antibacterial activities against A. baumanii 9010, A. baumanii 9011 and Citrobacter freundii (MICs of 40–49 µg/mL) (Tian et al. 2021). In another study, the novel carbazole alkaloid clausenal (102) was isolated from the leaves of Clausena heptaphylla. Clustered MICs of 6, 25 and 20 µg/mL were observed against E. coli, S. typhi and P. aeruginosa, respectively (Chakraborty et al. 1995). Ethanol extraction of the twigs and leaves of Kopsia hainanensis resulted in the isolation of two new aspidofractinine alkaloids, kopsiahainanins A and B (103, 104). These alkaloids showed antibacterial activity against E. coli, E. cloacae, P. aeruginosa, K. pneumoniae and S. dysenteriae. MIC values of 230, 150, 120, 130, and 120 µg/mL for compound 103 and MIC values of 260, 190, 140, 160 and 180 µg/mL for compound 104 were determined. The results showed that the improved cytotoxic and antibacterial activities could be related to the lactone bridge between C-6 and C-16 in the aspidofractinine alkaloidal skeleton (Chi et al. 2018). Cimanga et al. reported that four alkaloids, quindoline (105), hydroxycryptolepine (106), cryptolepine HC1 (107), and cryptolepine (108), from the root bark of Cryptolepis sanguinolenta showed antibacterial activity. The MICs of these alkaloids against E. coli were reported to be 125, 125, 125, and 62.5 µg/mL. Compound 106, with an MIC and MBC of 7.8 µg/mL, and compound 108, with an MIC of 125 µg/mL and an MBC of 250 µg/mL, were active against E. cloacae. The MIC and MBC of compounds 105 and 106 against K. pneumoniae were determined to be equal to or greater than 250 µg/mL. The MICs of all the alkaloids against P. vulgaris were 31, 125, 125 and 250 µg/mL. Only compound 108 was active against P. aeruginosa, with an MIC and MBC of 250 µg/mL. All of them were active against S. typhimurium (MICs = 250, 62.5, 125, and 62.5 µg/mL, respectively) (MBCs = 500, 62.5, 250, and 125 µg/mL, respectively) (Cimanga et al. 1996). Long et al. isolated a novel indole alkaloid, kopsifoline K (109), from the aerial parts of Kopsia fruticose. This alkaloid was found to be active against E. coli, with an MIC of 150 µg/mL (Long et al. 2018). In a study conducted by Navarro et al., dihydrosanguinarine (110), a benzophenanthridine alkaloid isolated from the chloroform extract of Bocconia arborea, was shown to be active against E. coli and P. mirabilis, with MICs of 150 and 75 μg/ml, respectively (Navarro and Delgado 1999). Sulfoscorzonin D (111), a new pyrrolidine alkaloid with a sulfated guaiane sesquiterpene lactone nucleus compound, was isolated from the extract of the aerial parts of Scorzonera divaricate. This alkaloid displayed activity against E. coli with an MIC of 25 μg/ml (Wu et al. 2018). Thirty-two alkaloids, including melokhanines A − J (112–121), euconolam (122), rhazinal (123), leuconodine C (124), leuconodine E (125), ( +)-eburnamonine (126), eburnamenine (127), O-methyl-16-epivincanol (128), O-methylvincanol (129), 14,15-dehydrovincanol (130), 16-epi-14,15-dehydrovincanol (131), 14,15-dehydrovincamine (132), 14,15-dehydroepivincamine (133), melodinine F (134), (+)-eburnamonine N(4)-oxide (135), melodinines A–C (136–138), 5c leuconicine B (139), leuconicine E (140), decarbomethoxydihydrogambirtannine (141), ajmalicine (142), and isositsirikine (143) isolated from Melodinus khasianus, exhibited significant antibacterial activity against P. aeruginosa ATCC 27,853 with MICs between 2 and 22 μg/ml (Cheng et al. 2016). It was indicated that 16,17,19,20–tetrahydro–2,16–dehydro–18–deoxyisostrychnine (144), a new strychnine alkaloid isolated from Psychotria pilifera, exhibited potential antibacterial activity equivalent to that of cefotaxime against various kinds of bacterial strains. These important results were related to E. coli strains with an MIC of 0.78 μg/ml (Liu et al. 2016). Didymellanosine (145) and ascolactone C (146), two macrocyclic alkaloids from the fungus Didymella sp. IEA-3B.1 associated with Terminalia catappa, have been reported to be significantly active against the gram-negative bacterium Acinetobacter baumannii (MIC = 3.1 µM) (Ariantari et al. 2020). Pyranoterreone C (147), an alkaloid isolated from the fungus Aspergillus amoenus, was found to be active against Acinetobacter baumannii, E. coli and E. cloacae (MIC = 4, 8 and 4 μg/ml, respectively) (Nord et al. 2020). A novel isoquinolone alkaloid, 5-hydroxy-8-methoxy-4-pheny lisoquinolin-1(2H)-one (148), from the fermentation of the endophytic fungus Penicillium sp. R22 in Nerium indicum displayed antibacterial activity against gram-negative bacteria, E. coli and P. aeruginosa, with an MIC of 125 µg/mL (Ma et al. 2017). In another study, JS-1 (149), a novel isoquinoline alkaloid isolated from the culture broth of Streptomyces sp. 8812, showed activity against B. bronchiseptica (MIC and MBC = 10 and 20 µg/mL), S. maltophilia, P. vulgaris, P. mirabilis, B. cepacia and A. baumanii (MIC and MBC = 160 µg/mL) (Solecka et al. 2009). Torres et al. isolated two novel tetracyclic alkylpiperidine alkaloids, namely, arenosclerins A and C (150 and 151) and haliclonacyclamine E (152), from the marine sponge Arenorclera brarilienrir. These alkaloids were evaluated for their antibacterial activity against gram-negative bacteria. The MICs of compounds 150 and 151 against E. coli were reported to be 100 µg/mL, while compounds 150, 151 and 152 showed activity against P. aeruginosa (MIC = 50, 50, and 200 µg/mL, respectively). The results showed that the bis-piperidine ring system and its stereochemical alteration are very important for the antibacterial activity of these alkaloids. This ring is different in these alkaloids (Torres et al. 2002). 6,7-Dihydroxy-5,10-dihydropyrrolo[1,2-b] isoquinoline-3 carboxylic acid (spathullin A) (153) and 5,10-dihydropyrrolo[1,2-b] isoquinoline-6,7-diol (spathullin B) (154) were identified from culture broths of Penicillium spathulatum Em19. These compounds showed activity against E. coli, A. baumannii, E. cloacae, K. pneumoniae and P. aeruginosa. The MICs of compound 153 were 15, 15, 15, 64, and > 64 µg/mL, and the MICs of compound 154 were 5, 5, 5, 32 and 64 µg/mL (Nord et al. 2019). Based on the results of another study, bis(indole) alkaloids of the topsentin class identified as deoxytopsentin (155), bromodeoxytopsentin (156), bromotopsentin (157), 4,5-dihydro-6″-deoxybromotopsentin (158), and hamacanthin class, hamacanthin A (159), trans-4,5-dihydrohamacanthin A (160), hamacanthin B (161), 6″-debromohamacanthin A (162), and 6″-debromohamacanthin B (163) from the marine sponge Spongosorites sp. showed antibacterial activity against P. vulgaris, 6.25, 25, 25, > 100, 0.78, 12.5. 3.1, 3.1, 50 µg/mL and 12.5, 100, 50, > 100, 3.1, 25, 6.2, 12.5 and 100 µg/mL for S. typhimurium, respectively. Compound 158 exhibited lower activity due to the 4,5-dihydrogenation of the imidazole ring. These results indicate that the substitution of the indole and imidazole rings in the topsentins affects the antibacterial activity. Moreover, compound 159, with a 3,6-disubstituted pyrazinone ring, has considerable activity relative to compound 161, with a corresponding 3,5-disubstituted pyrazinone ring. The antibacterial activity of hamacantins is also attributed to the 3,6-disubstituted-5,6-dihydro-1(2H)-pyrazinone skeleton (Oh et al. 2006). The antibacterial activities of six β-carboline alkaloids (164–169) of the eudistomin Y class from the Korean ascidian Synoicum sp. were evaluated. These compounds were more active against S. typhimurium (MICs = 50, 6.2, 0.39, 0.78, 0.39, 0.78 µg/mL, respectively) and P. vulgaris (MICs = 25, 6.25, 0.39, 1.56, 0.78, 0.78 µg/mL, respectively) than against E. coli (MICs =  > 100, 100, 50, 50, 50, 50 µg/mL, respectively) (Won et al. 2012). Six innovative alkaloids, named stylisines A–F (170–175), were identified from chromatographic separation of the bioactive fraction of the marine sponge Stylissa massa. These alkaloids showed low activity against E. coli, X. vesicatoria, P. lachrymans, A. tumefaciens and R. solanacearum (MIC ≥ 128 µg/mL) (Sun et al. 2018). Another strong antimicrobial compound, 6-formamide-chetomin (176) and chetomin (177), derived from the endophytic fungus Chaetomium sp. M336, had an MIC of 0.78 μg/ml against E. coli and S. typhimurium ATCC 6539 (Yu et al. 2018). One new potent anti-gram-negative compound, coralmycin A (178), was isolated from cultures of the myxobacteria Corallococcus coralloides M23. Compound 178 displayed significant antibacterial activity against E. faecalis, K. pneumoniae, P. aeruginosa, A. baumannii and E. coli (MICs: 0.01 to 4.0 μg/ml). The β-methoxyasparagine unit and the hydroxy group of the benzoic acid unit are critical for antibacterial activity (Kim et al. 2016). Several manzamine alkaloids (179–192) isolated from Indonesian Acanthostrongylophora sp. sponges showed a wide range of antibacterial activities against Proteus hauseri, E. coli, and Salmonella enterica (MIC: 2- > 100 µg/mL) (Kim et al. 2017). 3-Phenylpyrazin-2(1H)-one (193) and 3-O-methylviridicatin (194) isolated from the Streptomyces sp. TN82 strain exhibited potent antibacterial activity against S. typhimurium (MIC: 2.0 and 4.5 μg/ml, respectively), which was comparable to that of ampicillin (MIC: 4.0 μg/ml) and kanamycin (MIC: 12.5 μg/ml) (El Euch et al. 2018). The chemical structures of the alkaloids are shown in Fig. 6.

Fig. 6

Chemical structures of triterpenoids

As mentioned above, naturally occurring alkaloids, which can be used as chemical scaffolds for further exploration and as alternative antimicrobial agents, have good potential because of their antibacterial properties, especially against gram-negative bacteria.

Organosulfur allicin

Various bioactive compounds of garlic are responsible for its health properties. Among them, allicin (195), a natural organosulfur compound, is responsible for the pungent odor of garlic and has numerous antibiotic properties in the low range (μM) against gram-negative bacteria (Li et al. 2022). A previous study demonstrated that allicin could inhibit P. aeruginosa biofilm formation at a concentration of 128 µg/ml (Lihua et al. 2013). Other studies have confirmed similar results (Bjarnsholt et al. 2005; Li et al. 2018). Allicin has also been demonstrated to be effective against H. pylori in vivo (Haristoy et al. 2005). Its mechanism of action is due to the reaction of allicin with thiol groups of different enzymes to inhibit cysteine protease metabolism, as evidenced by the diminished inhibitory impacts of allicin caused by the development of cysteine and glutathione in the media (Chung 2006; Leontiev et al. 2018). These two mixes can interact with allicin disulfide bonds, resulting in the forestalling of bacterial cells. Overall, allicin could be considered a good candidate for functioning as a novel natural antibacterial agent, especially against H. pylori.

Sulforaphane

The isothiocyanate sulforaphane (196) can be found in cruciferous plants. Sulforaphane (Fig. 7) has shown powerful antibacterial and anticarcinogenic properties, especially against E. coli, K. pneumonia and P. aeruginosa, and more effectively against H. pylori (both in vitro and in vivo), which is known as a potential causal agent of stomach cancer (Benzekri et al. 2016; Azizi-Soleiman and Zamanian 2020). This substance has also been shown to be effective against E. coli through destruction of the cell membrane or ATP synthase inhibition (Wu et al. 2012). Sulforaphane can influence cell membrane penetration and material and energy digestion and restrain the combination of nucleic acid and protein [237]. It has additionally shown synergistic impacts with streptomycin against E. coli and P. aeruginosa (Nowicki et al. 2019). In a study by Nowicki et al., sulforaphane displayed remarkable antibacterial activity against clinical isolates of E. coli MG1655 and E. coli MG1655 ppGpp, with MIC values of 88.6 and 44.3 µg/mL, respectively (Nowicki et al. 2019). Sulforaphane has more than one target in bacterial cells, which indicates that it has good potential for use against pathogenic bacterial infections.

Fig. 7

Chemical structures of organosulfur compounds

Miscellaneous compounds

There are several other compounds with anti-gram-negative activities (Fig. 8). Olletotrichones A and C (197–198), which were isolated from the endophytic fungus Colletotrichum sp. and leaves of Buxus sinica, displayed strong antibacterial activity against E. coli (MIC = 1.0 and 5.0 μg/ml) (Wang et al. 2016). Cytosporin L (199), which is isolated from the gorgonian-derived fungus Eutypella sp., has inhibitory activity against the gram-negative bacterium E. aerogenes (MIC = 3.1 μM) (Liao et al. 2017). 15-Hydroxy-1,4,5,6-tetra-epi-koninginin G (200) isolated from Trichoderma koningiopsis shows potential activity against V. alginolyticus (MIC = 1.0 μg/ml) (Shi et al. 2020). Figure 9 shows a schematic representation of the mechanism of action of the selected natural products. In Table 1, potent antibacterial compounds and their mechanism of action are presented.

Fig. 8

Chemical structures of miscellaneous compounds

Fig. 9

The antimicrobial activity of selected natural compounds against gram-negative bacteria

Table 1 Selected natural compounds with antimicrobial activities against gram-negative bacteria (MICs < 256 µg/ml/µM)

Conclusions

The presence of antibiotic-resistant microorganisms, especially gram-negative strains, has become an important therapeutic problem in hospital- or community-acquired infections. To date, several new chemical drugs have been proposed to combat this problem. Therefore, there is a need to develop new antimicrobial agents and antibiotics for controlling antibiotic-resistant bacteria. Numerous studies have also identified effective natural substances that could be among the most important therapeutic tools for discovering new natural antibiotics. According to the current study, some of the compounds exhibited substantial anti-gram-negative activity with MICs lower than 10 μg/ml and could be the most important options for promising antibiotics in future complementary medicine. For instance, among terpenoids, two clerodane diterpenoids (43–44) isolated from Polyalthia longifolia have shown potent activity against a panel of gram-negative bacteria, E. coli, Klebsiella aerogenes, P. aeruginosa, P. putida, S. typhimurium, Sarcina lutea, and Nocardia sp., with MICs ranging from 0.78 to 6.2 µg/ml. Four triterpenoids (59–62) obtained from Dysoxylum densiflorum exhibited significant activity against five gram-negative bacteria, namely, E. coli, E. cloacae, K. pneumoniae, P. aeruginosa, and S. dysenteriae (MIC range, 1.0–2.9 μM). Artabotrine (94) and liridine (95), two alkaloids extracted from Artabotrys crassifolius, were active against K. pneumoniae with MIC values of 2.5 and 2.5 µg/mL, respectively. In the same class, two other compounds, 6-formamide-chetomin (176) and chetomin (177), derived from the endophytic fungus Chaetomium sp. M336, showed potent activity against E. coli and S. typhimurium, with an MIC of 0.78 μg/ml. Another alkaloid with potent anti-gram-negative activity, coralmycin A (178), which was isolated from cultures of the myxobacterium Corallococcus coralloides M23, showed strong activity against E. faecalis, K. pneumoniae, P. aeruginosa, A. baumannii and E. coli, with MICs ranging from 0.01 to 4.0 μg/ml. Olletotrichone A (197), obtained from the endophytic fungus Colletotrichum sp., showed potent activity against E. coli (MIC = 1.0 μg/ml). In addition, another endophytic compound (200) derived from Trichoderma koningiopsis exhibited potential activity against V. alginolyticus (MIC = 1.0 μg/ml). Some of the mentioned compounds were found to be effective antimicrobial agents or even more effective than tested commercial antibiotics. The current study provides value for identifying natural lead compounds for possible future development as anti-gram-negative agents.