Marine natural products and their synthetic analogs as promising antibiofilm agents for antibiotics discovery and development

Marine natural products as potential anti-Pseudomonas aeruginosa agents: challenges and advances

Antimicrobial resistance (AMR) has become a pressing need to address in the major global public health challenges, posing a serious threat to human health. Pseudomonas aeruginosa (PA) is one of the most concerning Gram-negative pathogens and is typically treated with broad-spectrum antibiotics. PA exhibits resistance to multiple antibiotics, multifactorial virulence, and dynamic hyperadaptation, which results in a particularly formidable challenge in eliminating PA from patients. The problem of drug resistance is becoming increasingly serious, and the development of new antibiotics is extremely lagging behind, resulting in no drug with a new structure and mechanism being approved for the treatment of infections caused by drug-resistant Gram-negative bacteria over the past half-century. Consequently, the development of new antibiotics is of utmost urgency and importance. Marine natural products (MNPs) have become an important source for developing new antibiotics due to their unique properties. So far, 44 potential molecules with significant anti-PA activity have been isolated from marine organisms, of which 19 have been reported as quorum-sensing system inhibitors (QSIs) with potential for further development. In this review, we provide a comprehensive summary of the current status of drug resistance, pathogenic mechanisms, and resistance mechanisms associated with PA infections. We also highlight the challenges and opportunities presented by MNPs in the development of anti-PA drugs, and offer recommendations to accelerate the antibiotic development process, thereby providing valuable insights for the study and exploitation of novel antibiotics.

Discovery, total synthesis, and biological evaluation of tyrcinnamins as antibacterial agents and tyrosinase activators

Microorganisms serve as critical resources for the discovery of new antibacterial drug leads. Herein, we report the screening, isolation, and identification of tyrcinnamin (1) from the endophytic Streptomyces sp. JS-B1. The total synthesis, biological evaluation, and structural-activity relationship study of tyrcinnamin and its synthetic derivatives led to the discovery of 7a, a promising lead compound with significant antibacterial activity, notable tyrosinase activation activity, and an excellent safety profile. The analysis of molecular docking of 7a with mushroom tyrosinase reveals that 7a may competitively occupy the binding site of l-DOPA on the surface of tyrosinase without interfering with the substrate binding at the active center, thereby reducing the ineffective occupancy of l-DOPA on the tyrosinase surface and improving the binding efficiency of l-DOPA at the active center. The structure of 7a represents a new chemical scaffold for the development of new antibiotics and tyrosinase activators, making valuable contributions to both drug discovery and cosmetics development.

Synthesis of Marine-Inspired Multifaceted DNA Damaging Spirooxindoles Combating NSCLC and Associated Bacterial Infection

Targeted therapeutics have gained prominence in combating non-small cell lung carcinoma (NSCLC) and opportunistic bacterial infections like Staphylococcus aureus (S. aureus). This study explores dual-acting marine-inspired spirooxindoles to limit NSCLC and opportunistic bacteria. Pharmacophoric motifs from antitumor and antibacterial marine products were merged into a new series of pyrazole-clubbed spirooxindoles via a stereoselective [3 + 2] cycloaddition reaction. MTT screening identified 4e, 4i, and 4p-4s as potent cytotoxic agents, with 4p showing exceptional activity (IC50 = 0.042 μM) and tumor selectivity (SI = 58.28). 4p exhibited antibacterial efficacy against S. aureus (MIC = 25 μg/mL). DNA damage studies using a terbium(III) chloride biosensor revealed 4p's ability to damage both calf thymus and S. aureus DNA at low concentrations. Docking simulations presumed that 4p binds between DNA strands, while apoptosis studies indicated it induced G1/S phase cell cycle arrest and increased A549 apoptosis by 33.65%. These findings highlight 4p as a promising lead for further studies.

A systematic review on the anti-microbial activities and structure-activity relationship (SAR) of quinoxaline derivatives

Anti-microbial resistance has become a serious global health issue affecting millions of people worldwide. Despite extensive drug discovery efforts aimed at identifying potent molecules for effective anti-microbial treatments, the emergence of superbugs remains a significant challenge. Thus, developing novel therapeutic agents is required to combat these evolving threats. The quinoxaline scaffold emerges as a promising heterocyclic framework for developing novel anti-microbial agents. It's simple, flexible structure, coupled with its bioisosteric relationship to extensively explored quinoline and naphthalene scaffolds, offers a potential avenue for circumventing bacterial resistance developed against these established classes. Hence it has sparked interest in researchers to develop novel antibiotics based on the quinoxaline core. This review focuses on the recent advances of quinoxaline derivatives as anti-microbial agents and their structure-activity relationship studies based on the literature published from 2015 to 2024. The systematic presentation of this information will assist researchers in identifying key substitution patterns around the quinoxaline nucleus, facilitating the development of structure-activity relationship (SAR), and guiding the design of novel anti-microbial drugs to combat the growing threat of anti-microbial resistance.

Nature-inspired Novel Quaternary Ammonium Compounds: Synthesis, Antibacterial and Antibiofilm Activity

Inspired by marine compounds isolated from sponges and the increased need for new effective antimicrobials, novel quaternary ammonium compounds with long alkyl chains (C8-C12) were designed and synthesized. Antibacterial and antibiofilm activity of new compounds was evaluated against six microbial strains (S. aureus, E. coli, and P. aeruginosa). All synthesized ammonium salts displayed antibacterial activity with MIC values ranging from 5.0 to 25.0 μg/mL. In addition, most compounds showed strong inhibition of biofilm formation of S. aureus ATCC 25923, P. aeruginosa PA01, and colistin-resistant P. aeruginosa (CRPA) at a concentration of 5.0 μg/mL. Ammonium salt 3 showed 100 % inhibitory activity against all tested bacterial biofilms except that of colistin-resistant S. aureus (CRSA).

The Effects of Marine Fungal Asterripeptides A-C on In Vitro and In Vivo Staphylococcus aureus Skin Infection

Objectives: This study aimed to investigate the in vitro and in vivo antibacterial and cytoprotective activities of marine fungal tripeptide derivatives with cinnamic acid moiety asterripeptides A-C (1-3). Methods: The antimicrobial and antibiofilm activities of asterripeptides A-C were tested using the Staphylococcus aureus ATCC 21027 strain. Human HaCaT keratinocytes infected with S. aureus were used for the in vitro investigation of the various aspects of the influence of asterripeptides A-C by lumino- and fluorospectrometry, ELISA, flow cytometry, Western blotting, and microscopy techniques. In the in vivo experiments, mice with burns and scalped S. aureus-infected wounds were used according to ethical committee resolution. Results: Asterripeptides A-C (10 µM) inhibited S. aureus growth and biofilm formation. Asterripeptides A-C increased the viability, proliferation, and migration of S. aureus-infected HaCaT cells and reduced the release of reactive oxygen species (ROS), NO, TNF-α, and IL-18. Asterripeptides A-C protected HaCaT cells against TNF-α-induced inflammation, decreased the transcriptional level of NF-κB in JB6 Cl41 cells, and increased the protein levels of Nrf2 and glutathione synthetase in HaCaT cells. More active asterripeptide C was tested in in vivo burn wounds and S. aureus-infected incised wounds. Asterripeptide C significantly enhanced wound healing, normalized cytokine levels and profiles of peripheral blood samples, and decreased S. aureus contamination of wounds and blood in mice with infected incised wounds. Conclusions: Taken together, these results confirm the dual antibacterial and Nrf2-dependent anti-inflammatory activities of asterripeptides A-C in in vitro and in vivo assays.

Decoding host cell interaction- and fluconazole-induced metabolic alterations and drug resistance in Candida auris

Candida auris is an emerging drug-resistant pathogen associated with high mortality rates. This study aimed to explore the metabolic alterations and associated pathogenesis and drug resistance in fluconazole-treated Candida auris-host cell interaction. Compared with controls, secreted metabolites from fluconazole-treated C. auris and fluconazole-treated C. auris-host cell co-culture demonstrated notable anti-Candida activity. Fluconazole caused significant reductions in C. auris cell numbers and aggregated phenotype. Metabolites produced by C. auris with potential fungal colonization, invasion, and host immune evasion effects were identified. Metabolites known to enhance biofilm formation produced during C. auris-host cell interaction were inhibited by fluconazole. Fluconazole enhanced the production of metabolites with biofilm inhibition activity, including behenyl alcohol and decanoic acid. Metabolites with potential Candida growth inhibition activity such as 2-palmitoyl glycerol, 1-tetradecanol, and 1-nonadecene were activated by fluconazole. Different patterns of proinflammatory cytokine expression presented due to fluconazole concentration and host cell type (fibroblasts versus macrophages). This highlights the immune response's complexity, emphasizing the necessity for additional research to comprehend cell-type-specific responses to antifungal therapies. Both host cell interaction and fluconazole treatment increased the expression of CDR1 and ERG11 genes, both associated with drug resistance. This study provides insights into pathogenesis in C. auris due to host cell interaction and fluconazole treatment. Understanding these interactions is crucial for enhancing fluconazole sensitivity and effectively combating C. auris.

Mechanisms of action of berberine hydrochloride in planktonic cells and biofilms of Pseudomonas aeruginosa

The increasing prevalence of extensively drug-and pan-drug-resistant Pseudomonas aeruginosa is a major concern for global public health. Therefore, it is crucial to develop novel antimicrobials that specifically target P. aeruginosa and its biofilms. In the present study, we determined that berberine hydrochloride inhibited the growth of planktonic bacteria as well as prevented the formation of biofilms. Moreover, we observed downregulation in the expression of pslA and pelA biofilm-related genes. Compared with existing antibiotics, berberine hydrochloride exhibits multiple modes of action against P. aeruginosa. Our findings suggest that berberine hydrochloride exerts its antimicrobial effects by damaging bacterial cell membranes, generating reactive oxygen species (ROS), and reducing intracellular adenosine triphosphate (ATP) levels. Furthermore, berberine hydrochloride showed minimal cytotoxicity and reduced susceptibility to drug resistance. In a mouse model of peritonitis, it significantly inhibited the growth of P. aeruginosa and exhibited a strong bacteriostatic action. In conclusion, berberine hydrochloride is a safe and effective antibacterial agent that inhibits the growth of P. aeruginosa.

Anti-quorum Sensing and Anti-biofilm Effect of Nocardiopsis synnemataformans RMN 4 (MN061002) Compound 2,6-Di-tert-butyl, 1,4-Benzoquinone Against Biofilm-Producing Bacteria

In this study, the anti-biofilm compound of 2,6-Di-tert-butyl, 1,4-benzoquinone was purified from Nocardiopsis synnemataformans (N. synnemataformans) RMN 4 (MN061002). To confirm the compound, various spectroscopy analyses were done including ultraviolet (UV) spectrometer, Fourier transform infrared spectroscopy (FTIR), analytical high-performance liquid chromatography (HPLC), preparative HPLC, gas chromatography-mass spectroscopy (GC-MS), liquid chromatography-mass spectroscopy (LC-MS), and 2D nuclear magnetic resonance (NMR). Furthermore, the purified compound was shown 94% inhibition against biofilm-producing Proteus mirabilis (P. mirabilis) (MN396686) at 70 µg/mL concentrations. Furthermore, the metabolic activity, exopolysaccharide damage, and hydrophobicity degradation results of identified compound exhibited excellent inhibition at 100 µg/mL concentration. Furthermore, the confocal laser scanning electron microscope (CLSM) and scanning electron microscope (SEM) results were shown with intracellular damages and architectural changes in bacteria. Consecutively, the in vivo toxicity effect of the compound against Artemia franciscana (A. franciscana) was shown to have a low mortality rate at 100 µg/mL. Finally, the molecular docking interaction between the quorum sensing (QS) genes and identified compound clearly suggested that the identified compound 2,6-Di-tert-butyl, 1,4-benzoquinone has anti-quorum sensing and anti-biofilm activities against P. mirabilis (MN396686).

Modified oxylipins as inhibitors of biofilm formation in Staphylococcus epidermidis

New approaches to combating microbial drug resistance are being sought, with the discovery of biofilm inhibitors considered as alternative arsenal for treating infections. Natural products have been at the forefront of antimicrobial discovery and serve as inspiration for the design of new antibiotics. We probed the potency, selectivity, and mechanism of anti-biofilm activity of modified oxylipins inspired by the marine natural product turneroic acid. Structure-activity relationship (SAR) evaluation revealed the importance of the trans-epoxide moiety, regardless of the position, for inhibiting biofilm formation. trans-12,13-epoxyoctadecanoic acid (1) and trans-9,10 epoxyoctadecanoic acid (4) selectively target the early stage of biofilm formation, with no effect on planktonic cells. These compounds interrupt the formation of a protective polysaccharide barrier by significantly upregulating the ica operon's transcriptional repressor. This was corroborated by docking experiment with SarA and scanning electron micrographs showing reduced biofilm aggregates and the absence of thread-like structures of extrapolymeric substances. In silico evaluation revealed that 1 and 4 can interfere with the AgrA-mediated communication language in Staphylococci, typical to the diffusible signal factor (DSF) capacity of lipophilic chains.

Nanocomposites against Pseudomonas aeruginosa biofilms: Recent advances, challenges, and future prospects

Pseudomonas aeruginosa is an opportunistic bacterial pathogen that causes life-threatening and persistent infections in immunocompromised patients. It is the culprit behind a variety of hospital-acquired infections owing to its multiple tolerance mechanisms against antibiotics and disinfectants. Biofilms are sessile microbial aggregates that are formed as a result of the cooperation and competition between microbial cells encased in a self-produced matrix comprised of extracellular polymeric constituents that trigger surface adhesion and microbial aggregation. Bacteria in biofilms exhibit unique features that are quite different from planktonic bacteria, such as high resistance to antibacterial agents and host immunity. Biofilms of P. aeruginosa are difficult to eradicate due to intrinsic, acquired, and adaptive resistance mechanisms. Consequently, innovative approaches to combat biofilms are the focus of the current research. Nanocomposites, composed of two or more different types of nanoparticles, have diverse therapeutic applications owing to their unique physicochemical properties. They are emerging multifunctional nanoformulations that combine the desired features of the different elements to obtain the highest functionality. This review assesses the recent advances of nanocomposites, including metal-, metal oxide-, polymer-, carbon-, hydrogel/cryogel-, and metal organic framework-based nanocomposites for the eradication of P. aeruginosa biofilms. The characteristics and virulence mechanisms of P. aeruginosa biofilms, as well as their devastating impact and economic burden are discussed. Future research addressing the potential use of nanocomposites as innovative anti-biofilm agents is emphasized. Utilization of nanocomposites safely and effectively should be further strengthened to confirm the safety aspects of their application.

Investigating the antiviral therapeutic potentialities of marine polycyclic lamellarin pyrrole alkaloids as promising inhibitors for SARS-CoV-2 and Zika main proteases (Mpro)

The new coronavirus variant (SARS-CoV-2) and Zika virus are two world-wide health pandemics. Along history, natural products-based drugs have always crucially recognized as a main source of valuable medications. Considering the SARS-CoV-2 and Zika main proteases (Mpro) as the re-production key element of the viral cycle and its main target, herein we report an intensive computer-aided virtual screening for a focused list of 39 marine lamellarins pyrrole alkaloids, against SARS-CoV-2 and Zika main proteases (Mpro) using a set of combined modern computational methodologies including molecular docking (MDock), molecule dynamic simulations (MDS) and structure-activity relationships (SARs) as well. Indeed, the molecular docking studies had revealed four promising marine alkaloids including [lamellarin H (14)/K (17)] and [lamellarin S (26)/Z (39)], according to their notable ligand-protein energy scores and relevant binding affinities with the SARS-CoV-2 and Zika (Mpro) pocket residues, respectively. Consequentially, these four chemical hits were further examined thermodynamically though investigating their MD simulations at 100 ns, where they showed prominent stability within the accommodated (Mpro) pockets. Moreover, in-deep SARs studies suggested the crucial roles of the rigid fused polycyclic ring system, particularly aromatic A- and F- rings, position of the phenolic -OH and δ-lactone functionalities as essential structural and pharmacophoric features. Finally, these four promising lamellarins alkaloids were investigated for their in-silico ADME using the SWISS ADME platform, where they displayed appropriated drug-likeness properties. Such motivating outcomes are greatly recommending further in vitro/vivo examinations regarding those lamellarins pyrrole alkaloids (LPAs).Communicated by Ramaswamy H. Sarma.

Synthesis and in vitro evaluation of antibacterial and antibiofilm activities of novel triphenylphosphonium-functionalized substituted pyrimidines

The increase in the prevalence of antibiotic-resistant pathogens leads to a decrease in the number of antimicrobial agents for the treatment of infections and prompts researchers to search for new effective antimicrobial drugs. This study reports the synthesis of novel triphenylphosphonium-functionalized substituted pyrimidines and in vitro evaluation of their antibacterial and antibiofilm activity. Most of the synthesized derivatives showed high antibacterial activity (MIC = 0.39-1.56 μg/mL) against the methicillin-resistant strain of S. aureus 222. Compounds 2a and 11 exhibited a high level of antibiofilm activity against S. aureus 222 and E. coli 311. The triphenylphosphonium-containing pyrimidines 11 and 2a reduced S. aureus 222 biofilm formation by 99.1% and 95.8%, respectively. In addition, compound 2a was the most active against E. coli 311 biofilm formation (the biomass decreased by 98.4%).

Antibiofilm activity of marine microbial natural products: potential peptide- and polyketide-derived molecules from marine microbes toward targeting biofilm-forming pathogens

Controlling and treating biofilm-related infections is challenging because of the widespread presence of multidrug-resistant microbes. Biofilm, a naturally occurring matrix of microbial aggregates, has developed intricate and diverse resistance mechanisms against many currently used antibiotics. This poses a significant problem, especially for human health, including clinically chronic infectious diseases. Thus, there is an urgent need to search for and develop new and more effective antibiotics. As the marine environment is recognized as a promising reservoir of new biologically active molecules with potential pharmacological properties, marine natural products, particularly those of microbial origin, have emerged as a promising source of antibiofilm agents. Marine microbes represent an untapped source of secondary metabolites with antimicrobial activity. Furthermore, marine natural products, owing to their self-defense mechanisms and adaptation to harsh conditions, encompass a wide range of chemical compounds, including peptides and polyketides, which are primarily found in microbes. These molecules can be exploited to provide novel and unique structures for developing alternative antibiotics as effective antibiofilm agents. This review focuses on the possible antibiofilm mechanism of these marine microbial molecules against biofilm-forming pathogens. It provides an overview of biofilm development, its recalcitrant mode of action, strategies for the development of antibiofilm agents, and their assessments. The review also revisits some selected peptides and polyketides from marine microbes reported between 2016 and 2023, highlighting their moderate and considerable antibiofilm activities. Moreover, their antibiofilm mechanisms, such as adhesion modulation/inhibition targeting biofilm-forming pathogens, quorum sensing intervention and inhibition, and extracellular polymeric substance disruption, are highlighted herein.

Genus Litophyton: A Hidden Treasure Trove of Structurally Unique and Diversely Bioactive Secondary Metabolites

Marine soft corals are prolific sources of various natural products that have served as a wealthy reservoir of diverse chemical scaffolds with potential as new drug leads. The genus Litophyton contains almost 100 species but only a small proportion of them has been chemically investigated, which calls for more attentions from global researchers. In the current work, 175 secondary metabolites have been discussed, drawing from published data spanning almost five decades, up to July 2023. The studied species of the genus Litophyton resided in various tropical and temperate regions and encompassed a broad range of biologically active natural products including terpenes, steroids, nitrogen-containing metabolites, lipids, and other metabolites. A wide spectrum of pharmacological effects of these compounds had been evaluated, such as cytotoxic, antiviral, antibacterial, antifungal, anti-malarial, antifeedant, anti-inflammatory, molluscicidal, PTP1B inhibitory, insect growth inhibitory, and neuroprotective activities. This review aims to offer an up-to-date survey of the literature and provide a comprehensive understanding of the chemical structures, taxonomical distributions, and biological activities of the reported metabolites from the title genus whenever available.

Exploring Possible Ways to Enhance the Potential and Use of Natural Products through Nanotechnology in the Battle against Biofilms of Foodborne Bacterial Pathogens

Biofilms enable pathogenic bacteria to survive in unfavorable environments. As biofilm-forming pathogens can cause rapid food spoilage and recurrent infections in humans, especially their presence in the food industry is problematic. Using chemical disinfectants in the food industry to prevent biofilm formation raises serious health concerns. Further, the ability of biofilm-forming bacterial pathogens to tolerate disinfection procedures questions the traditional treatment methods. Thus, there is a dire need for alternative treatment options targeting bacterial pathogens, especially biofilms. As clean-label products without carcinogenic and hazardous potential, natural compounds with growth and biofilm-inhibiting and biofilm-eradicating potentials have gained popularity as natural preservatives in the food industry. However, the use of these natural preservatives in the food industry is restricted by their poor availability, stability during food processing and storage. Also there is a lack of standardization, and unattractive organoleptic qualities. Nanotechnology is one way to get around these limitations and as well as the use of underutilized bioactives. The use of nanotechnology has several advantages including traversing the biofilm matrix, targeted drug delivery, controlled release, and enhanced bioavailability, bioactivity, and stability. The nanoparticles used in fabricating or encapsulating natural products are considered as an appealing antibiofilm strategy since the nanoparticles enhance the activity of the natural products against biofilms of foodborne bacterial pathogens. Hence, this literature review is intended to provide a comprehensive analysis of the current methods in nanotechnology used for natural products delivery (biofabrication, encapsulation, and nanoemulsion) and also discuss the different promising strategies employed in the recent and past to enhance the inhibition and eradication of foodborne bacterial biofilms.

Innovative Strategies to Overcome Antimicrobial Resistance and Tolerance

Antimicrobial resistance and tolerance are natural phenomena that arose due to evolutionary adaptation of microorganisms against various xenobiotic agents. These adaptation mechanisms make the current treatment options challenging as it is increasingly difficult to treat a broad range of infections, associated biofilm formation, intracellular and host adapted microbes, as well as persister cells and microbes in protected niches. Therefore, novel strategies are needed to identify the most promising drug targets to overcome the existing hurdles in the treatment of infectious diseases. Furthermore, discovery of novel drug candidates is also much needed, as few novel antimicrobial drugs have been introduced in the last two decades. In this review, we focus on the strategies that may help in the development of innovative small molecules which can interfere with microbial resistance mechanisms. We also highlight the recent advances in optimization of growth media which mimic host conditions and genome scale molecular analyses of microbial response against antimicrobial agents. Furthermore, we discuss the identification of antibiofilm molecules and their mechanisms of action in the light of the distinct physiology and metabolism of biofilm cells. This review thus provides the most recent advances in host mimicking growth media for effective drug discovery and development of antimicrobial and antibiofilm agents.

Natural products as antivibrio agents: insight into the chemistry and biological activity

Vibriosis causes serious problems and economic loss in aquaculture and human health. Investigating natural products as antivibrio agents has gained more attention to combat vibriosis. The present review highlights the chemical diversity of antivibrio isolated from bacteria, fungi, plants, and marine organisms. Based on the study covering the literature from 1985-2021, the chemical diversity ranges from alkaloids, terpenoids, polyketides, sterols, and peptides. The mechanisms of action are included inhibiting growth, interfering with biofilm formation, and disrupting of quorum sensing. Relevant summaries focusing on the source organisms and the associated bioactivity of different chemical classes are also provided. Further research on in vivo studies, toxicity, and clinical is required for the application in aquaculture and human health.

Screening of Bioactive Compounds from Endophytic Marine-Derived Fungi in Saudi Arabia: Antimicrobial and Anticancer Potential

Nowadays, endophytic fungi represent a rich source of biological active compounds. In the current study, twelve endophytic fungal species were isolated from Avicennia marina leaves. From the isolates, Aspergillus niger, Penicillium rubens and Alternaria alternata recorded the highest isolation frequency (80%), relative density (12.5%) and antimicrobial activity. The antimicrobial and anticancer activities of P. rubens were more effective than those of A. niger and A. alternata; therefore, its identification was confirmed via the ITS rRNA gene. Filtrate extracts of P. rubens, A. alternata and A. niger were analyzed using GC-MS and showed different detected constituents, such as acetic acid ethyl ester, N-(4,6-Dimethyl-2-pyrimidinyl)-4-(4-nitrobenzylideneamino) benzenesulfonamide, 1,2-benzenedicarboxylic acid, hexadecanoic acid and octadecanoic acid. Filtrate extract of P. rubens exhibited the presence of more compounds than A. alternata and A. niger. Bacillus subtilis, Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, Candida albicans and Aspergillus fumigatus were more inhibited by P. rubens extract than A. alternata or A. niger, with inhibition zones of 27.2 mm, 22.21 mm, 26.26 mm, 27.33 mm, 28.25 mm and 8.5 mm, respectively. We observed negligible cytotoxicity of P. rubens extract against normal cells of human lung fibroblasts (WI-38 cell line), unlike A. alternata and A. niger extracts. Proliferation of prostate cancer (PC-3) was inhibited using P. rubens extract, exhibiting mortality levels of 75.91% and 76.2% at 200 µg/mL and 400 µg/mL of the extract. Molecular docking studies against the crystal structures of C. albicans (6TZ6) and the cryo-EM structure of B. subtilis (7CKQ) showed significant interactions with benzenedicarboxylic acid and N-(4,6-dimethyl-2-pyrimidinyl)-4-(4-nitrobenzylideneamino) benzenesulfonamide as a constituent of P. rubens extract. N-(4,6-dimethyl-2-pyrimidinyl)-4-(4-nitrobenzylideneamino) benzenesulfonamide had the highest scores of −6.04905 kcal/mol and −6.590 kcal/mol towards (6tz6) and (7CKQ), respectively.