Review: Structure-Activity Relationship of Antimicrobial Peptoids

Exploring the impact of bioactive peptides from fermented Milk proteins: A review with emphasis on health implications and artificial intelligence integration

This review explores the health benefits of bioactive peptides (BAPs) from fermented milk proteins, emphasizing the transformative role of artificial intelligence (AI) and machine learning (ML) in advancing this field. BAPs exhibit diverse biological activities, including antimicrobial, antihypertensive, antioxidant, and immunomodulatory effects, making them promising for functional foods and nutraceuticals. However, challenges such as stability, bioavailability, and cost-effective production remain. This review highlights how AI/ML-driven tools, including data mining, sequence analysis, and predictive modeling, revolutionize peptide discovery, optimize fermentation, and enable personalized nutrition. By accelerating the identification of novel peptides and enhancing production efficiency, AI/ML offers innovative solutions to overcome existing limitations. The integration of AI/ML not only improves research efficiency but also opens new avenues for personalized nutrition and therapeutic applications. This review underscores the potential of interdisciplinary collaboration to harness the benefits of BAPs fully, driving future advancements in functional foods and health promotion.

Discovery of ultra short β-peptoids with selective activity against drug-resistant Mycobacterium tuberculosis

There is an urgent need to develop new anti-tuberculosis (anti-TB) drugs to tackle drug-resistant strains of Mycobacterium tuberculosis (M.tb). Whereas antimicrobial peptides (AMPs) have received attention because of their antibacterial properties, oligo-N-substituted glycines (peptoids) are now seen as favorable alternatives to AMPs because they are more stable and less vulnerable to protease degradation, less expensive to produce, and better suited to potential pharmaceutical adoption and development. In this work, therefore, we designed, synthesized, and screened 22 new α- and β-peptoids against drug susceptible M. tb strain H37Rv using the Microplate Alamar Blue assay (MABA) to evaluate minimum inhibitory concentration (MIC). Eight compounds (JC5, MM2, MM5, MM9, MM10, MM11, JF11, and JF13) had MICs of less than 10 μg/ml, the most potent of which were JC5 and MM2, with MICs of 1.48 μg/ml and 2.97 μg/ml, respectively. JC5 and MM2 also retained potency against strains mono-resistant to isoniazid and rifampin, and against five of the global M. tb clade representatives. Furthermore, peptoids JC5 and MM2 showed minimum bactericidal concentration (MBC) of 3.02 μg/ml and 5.48 μg/ml respectively. Intracellular activity by luminescence showed a macrophage EC90 of less than 10 μg/ml for both JC5 and MM2. In addition, both compounds showed remarkable narrow spectrum activity. Selectivity with respect to Vero cells was modest but sufficient to consider these classes of alpha and beta-peptoids as good leads for further development of anti-TB drugs.

A biofilm-targeting lipo-peptoid to treat Pseudomonas aeruginosa and Staphylococcus aureus co-infections

Antibiotic-resistant bacterial infections are a significant clinical challenge, especially when involving multiple species. Antimicrobial peptides and their synthetic analogues, peptoids, which target bacterial cell membranes as well as intracellular components, offer potential solutions. We evaluated the biological activities of novel peptoids TM11-TM20, which include an additional charged NLys residue, against multidrug-resistant Pseudomonas aeruginosa and Staphylococcus aureus, both in vitro and in vivo. Building on insights from previously reported compounds TM1-TM10, the lipo-peptoid TM18, which forms self-assembled ellipsoidal micelles, demonstrated potent antimicrobial, anti-biofilm, and anti-abscess activity. Transcriptome sequencing (RNA-seq) revealed that TM18 disrupted gene expression pathways linked to antibiotic resistance and tolerance, and biofilm formation in both pathogens. Under dual-species conditions, TM18 induced overlapping but attenuated transcriptional changes, suggesting a priming effect that enhances bacterial tolerance. In a murine skin infection model, TM18 significantly reduced dermonecrosis and bacterial burden in mono-species infections. When combined with the antibiotic meropenem, they synergistically nearly cleared co-infections. Our findings highlight that TM18 has potential as a novel therapeutic for combating antibiotic-resistant pathogens and associated biofilm-driven tolerance.

To Transfer or Not to Transfer an Electron: Anionic Metal Centers Reveal Dual Functionality for Polymerization Reactions

Catalysts with anionic metal centers have recently been proposed to enhance the performance of various chemical processes. Here, we focus on the reactivity of Co(CO)4- for the polymerization of aziridine and carbon monoxide to form polypeptoids, motivated by earlier experimental studies. We used multi-reference and density functional theory methods to investigate possible reaction mechanisms and provide insights into the role of the negatively charged cobalt center. Two different reaction paths were identified. In the first path, Co- acts as a nucleophile, donating an electron pair to the reaction substrate, while in the second path, it performs a single electron transfer to the substrate, initiating radical polymerization. The difference in the activation barriers for the two key steps is small and falls within the accuracy of our calculations. As suggested in the literature, solvent effects can play a primary role in determining the outcomes of such reactions. Future investigations will involve different metals or ligands and will investigate the effects of these two reaction paths on other chemical transformations.

Harnessing marine antimicrobial peptides for novel therapeutics: A deep dive into ocean-derived bioactives

Marine antimicrobial peptides (AMPs) are potent bioactive compounds with broad-spectrum activity against bacteria, viruses, and fungi, offering a promising alternative to traditional antibiotics. These small, cationic, and amphiphilic peptides (3-50 amino acids) are key components of marine organisms' immune defenses, adapted to harsh oceanic environments. Discovered in the 1980s, marine AMPs have garnered interest for their unique structures and potential applications in human health. However, despite the ocean's vast biodiversity, they remain underexplored compared to land-based AMPs. This review emphasizes the therapeutic potential of marine AMPs, including their modes of action, structural variety, and applications in drug development, tissue regeneration, and cancer treatment. Moreover, it discusses their antibacterial, antiviral, antifungal, and antiparasitic properties. Additionally, the review addresses strategies to enhance the therapeutic potential of marine AMPs and the challenges associated with their development. By examining the promising future of marine AMPs, this review aims to pave the way for new approaches to combat antimicrobial resistance and develop innovative treatments for various infectious diseases. The potential of marine AMPs as the "medicine bank of the new millennium" remains vast, providing a valuable resource for future drug discovery and sustainable practices across industries.

Recent advances in peptoids as promising antimicrobial agents to target diverse microbial species

The emergence of multidrug-resistant microbial species has become a global health concern, calling for novel antimicrobial agents. Peptoids, a class of synthetic peptidomimetics with unique structural properties, exhibit antimicrobial activity against a broad-spectrum of microbes, in addition to their stability to enzymatic degradation, selectivity, and relative ease of synthesis. Thus, peptoids have great potential in combating various drug-resistant pathogenic microbes. This review provides a comprehensive analysis of the recent advances in utilizing peptoids as effective antimicrobial agents against a wide range of bacteria, fungi, viruses, and parasites. In addition, some of the synthetic strategies and antimicrobial mechanisms are discussed. The imperfections of antimicrobial peptoids and the defects in current antimicrobial peptoids research are pointed out and promising directions for future development in peptoids are highlighted, to pave the way for innovating better antimicrobial peptoids to address the challenges posed by multidrug-resistant microbial species.

Self-Assembling and Pore-Forming Peptoids as Antimicrobial Biomaterials

Bacterial infections have been a serious threat to mankind throughout history. Natural antimicrobial peptides (AMPs) and their membrane disruption mechanism have generated immense interest in the design and development of synthetic mimetics that could overcome the intrinsic drawbacks of AMPs, such as their susceptibility to proteolytic degradation and low bioavailability. Herein, by exploiting the self-assembly and pore-forming capabilities of sequence-defined peptoids, we discovered a family of low-molecular weight peptoid antibiotics that exhibit excellent broad-spectrum activity and high selectivity toward a panel of clinically significant Gram-positive and Gram-negative bacterial strains, including vancomycin-resistant Enterococcus faecalis (VREF), methicillin-resistant Staphylococcus aureus (MRSA), methicillin-resistant Staphylococcus epidermidis (MRSE), Escherichia coli, Pseudomonas aeruginosa, and Klebsiella pneumoniae. Tuning the peptoid side chain chemistry and structure enabled us to tune the efficacy of antimicrobial activity. Mechanistic studies using transmission electron microscopy (TEM), bacterial membrane depolarization and lysis, and time-kill kinetics assays along with molecular dynamics simulations reveal that these peptoids kill both Gram-positive and Gram-negative bacteria through a membrane disruption mechanism. These robust and biocompatible peptoid-based antibiotics can provide a valuable tool for combating emerging drug resistance.

Self-assembling short peptide amphiphiles as versatile delivery agents: a new frontier in antibacterial research

Self-assembling short peptide amphiphiles, crafted through a minimalistic approach, spontaneously generate well-ordered nanostructures, facilitating the creation of precise nanostructured biomaterials for diverse biomedical applications. The seamless integration of bioactive metal ions and nanoparticles endows them with the potential to serve as pioneering materials in combating bacterial infections. Nanomanipulation of these molecules' binary structures enables effective penetration of membranes, forming structured nanoarchitectures with antibacterial properties. Through a comprehensive exploration, we attempt to reveal the innovative potential of short peptide amphiphiles, particularly in conjugation with metal cations and nanoparticles, offering insights for future research trajectories.

Non-canonical amino acid bioincorporation into antimicrobial peptides and its challenges

The rise of antimicrobial resistance and multi-drug resistant pathogens has necessitated explorations for novel antibiotic agents as the discovery of conventional antibiotics is becoming economically less viable and technically more challenging for biopharma. Antimicrobial peptides (AMPs) have emerged as a promising alternative because of their particular mode of action, broad spectrum and difficulty that microbes have in becoming resistant to them. The AMPs bacitracin, gramicidin, polymyxins and daptomycin are currently used clinically. However, their susceptibility to proteolytic degradation, toxicity profile, and complexities in large-scale manufacture have hindered their development. To improve their proteolytic stability, methods such as integrating non-canonical amino acids (ncAAs) into their peptide sequence have been adopted, which also improves their potency and spectrum of action. The benefits of ncAA incorporation have been made possible by solid-phase peptide synthesis. However, this method is not always suitable for commercial production of AMPs because of poor yield, scale-up difficulties, and its non-'green' nature. Bioincorporation of ncAA as a method of integration is an emerging field geared towards tackling the challenges of solid-phase synthesis as a green, cheaper, and scalable alternative for commercialisation of AMPs. This review focusses on the bioincorporation of ncAAs; some challenges associated with the methods are outlined, and notes are given on how to overcome these challenges. The review focusses particularly on addressing two key challenges: AMP cytotoxicity towards microbial cell factories and the uptake of ncAAs that are unfavourable to them. Overcoming these challenges will draw us closer to a greater yield and an environmentally friendly and sustainable approach to make AMPs more druggable.

Dimeric peptoids as antibacterial agents

Building upon our previous study on peptoid-based antibacterials which showed good activity against Gram-positive bacteria only, herein we report the synthesis of 34 dimeric peptoid compounds and the investigation of their activity against Gram-positive and Gram-negative pathogens. The newly designed peptoids feature a di-hydrophobic moiety incorporating phenyl, bromo-phenyl, and naphthyl groups, combined with variable lengths of cationic units such as amino and guanidine groups. The study also underscores the pivotal interplay between hydrophobicity and cationicity in optimizing efficacy against specific bacteria. The bromophenyl dimeric guanidinium peptoid compound 10j showed excellent activity against S. aureus 38 and E. coli K12 with MIC of 0.8 μg mL-1 and 6.2 μg mL-1, respectively. Further investigation into the mechanism of action revealed that the antibacterial effect might be attributed to the disruption of bacterial cell membranes, as suggested by tethered bilayer lipid membranes (tBLMs) and cytoplasmic membrane permeability studies. Notably, these promising antibacterial agents exhibited negligible toxicity against mammalian red blood cells. Additionally, the study explored the potential of 12 active compounds to disrupt established biofilms of S. aureus 38. The most effective biofilm disruptors were ethyl and octyl-naphthyl guanidinium peptoids (10c and 10 k). These compounds 10c and 10 k disrupted the established biofilms of S. aureus 38 with 51 % at 4x MIC (MIC = 17.6 μg mL-1 and 11.2 μg mL-1) and 56 %-58 % at 8x MIC (MIC = 35.2 μg mL-1 and 22.4 μg mL-1) respectively. Overall, this research contributes insights into the design principles of cationic dimeric peptoids and their antibacterial activity, with implications for the development of new antibacterial compounds.

Antiviral Effect of Antimicrobial Peptoid TM9 and Murine Model of Respiratory Coronavirus Infection

New antiviral agents are essential to improving treatment and control of SARS-CoV-2 infections that can lead to the disease COVID-19. Antimicrobial peptoids are sequence-specific oligo-N-substituted glycine peptidomimetics that emulate the structure and function of natural antimicrobial peptides but are resistant to proteases. We demonstrate antiviral activity of a new peptoid (TM9) against the coronavirus, murine hepatitis virus (MHV), as a closely related model for the structure and antiviral susceptibility profile of SARS-CoV-2. This peptoid mimics the human cathelicidin LL-37, which has also been shown to have antimicrobial and antiviral activity. In this study, TM9 was effective against three murine coronavirus strains, demonstrating that the therapeutic window is large enough to allow the use of TM9 for treatment. All three isolates of MHV generated infection in mice after 15 min of exposure by aerosol using the Madison aerosol chamber, and all three viral strains could be isolated from the lungs throughout the 5-day observation period post-infection, with the peak titers on day 2. MHV-A59 and MHV-A59-GFP were also isolated from the liver, heart, spleen, olfactory bulbs, and brain. These data demonstrate that MHV serves as a valuable natural murine model of coronavirus pathogenesis in multiple organs, including the brain.

LL-37: Structures, Antimicrobial Activity, and Influence on Amyloid-Related Diseases

Antimicrobial peptides (AMPs), as well as host defense peptides (HDPs), constitute the first line of defense as part of the innate immune system. Humans are known to express antimicrobial precursor proteins, which are further processed to generate AMPs, including several types of α/β defensins, histatins, and cathelicidin-derived AMPs like LL37. The broad-spectrum activity of AMPs is crucial to defend against infections caused by pathogenic bacteria, viruses, fungi, and parasites. The emergence of multi-drug resistant pathogenic bacteria is of global concern for public health. The prospects of targeting antibiotic-resistant strains of bacteria with AMPs are of high significance for developing new generations of antimicrobial agents. The 37-residue long LL37, the only cathelicidin family of AMP in humans, has been the major focus for the past few decades of research. The host defense activity of LL37 is likely underscored by its expression throughout the body, spanning from the epithelial cells of various organs-testis, skin, respiratory tract, and gastrointestinal tract-to immune cells. Remarkably, apart from canonical direct killing of pathogenic organisms, LL37 exerts several other host defense activities, including inflammatory response modulation, chemo-attraction, and wound healing and closure at the infected sites. In addition, LL37 and its derived peptides are bestowed with anti-cancer and anti-amyloidogenic properties. In this review article, we aim to develop integrative, mechanistic insight into LL37 and its derived peptides, based on the known biophysical, structural, and functional studies in recent years. We believe that this review will pave the way for future research on the structures, biochemical and biophysical properties, and design of novel LL37-based molecules.

Peptoids: Smart and Emerging Candidates for the Diagnosis of Cancer, Neurological and Autoimmune Disorders

Early detection of fatal and disabling diseases such as cancer, neurological and autoimmune dysfunctions is still desirable yet challenging to improve quality of life and longevity. Peptoids (N-substituted glycine oligomers) are a relatively new class of peptidomimetics, being highly versatile and capable of mimicking the architectures and the activities of the peptides but with a marked resistance to proteases and a propensity to cross the cellular membranes over the peptides themselves. For these properties, they have gained an ever greater interest in applications in bioengineering and biomedical fields. In particular, the present manuscript is to our knowledge the only review focused on peptoids for diagnostic applications and covers the last decade's literature regarding peptoids as tools for early diagnosis of pathologies with a great impact on human health and social behavior. The review indeed provides insights into the peptoid employment in targeted cancer imaging and blood-based screening of neurological and autoimmune diseases, and it aims to attract the scientific community's attention to continuing and sustaining the investigation of these peptidomimetics in the diagnosis field considering their promising peculiarities.