Advances in Antimicrobial Peptides: Mechanisms, Design Innovations, and Biomedical Potential

This comprehensive review explores the advancements in the study of antimicrobial peptides (AMPs), highlighting their potential as promising alternatives to conventional antibiotics in the context of growing antibiotic resistance. AMPs are small molecular proteins found ubiquitously in nature, exhibiting broad-spectrum antimicrobial activity, including antibacterial, antiviral, and antifungal effects, and are vital components of the innate immune system. Due to their non-specific membrane-disrupting mechanism, AMPs are emerging as effective candidates for novel anti-infective agents. The integration of AMPs with biomaterials, such as nanoparticles, liposomes, polymers, and hydrogels, enhances their stability and efficacy while offering multifunctional therapeutic benefits. These combinations promote diverse antibacterial mechanisms, including membrane disruption, intracellular metabolic interference, cell wall modulation, and immune system activation. Despite challenges, such as toxicity, stability, and resistance, innovative strategies including computer-aided design and structural modification show promise in optimizing AMPs' activity, targeting precision, and biocompatibility. The potential for AMPs in clinical applications remains highly promising, with significant opportunities for overcoming antimicrobial resistance through novel AMP-based therapeutic strategies.

Antimicrobial Peptides as Immunomodulators and Antimycobacterial Agents to Combat Mycobacterium tuberculosis: a Critical Review

Tuberculosis (TB) is a devastating disease foisting a significantly high morbidity, prepotent in low- and middle-income developing countries. Evolution of drug resistance among Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, has made the TB treatment more complicated. The protracted nature of present TB treatment, persistent and tolerant Mtb populations, interaction with antiretroviral therapy and existing toxicity concerned with conventional anti-TB drugs are the four major challenges inflicted with emergence of drug-resistant mycobacterial strains, and the standard medications are unable to combat these strains. These factors emphasize an exigency to develop new drugs to overcome these barriers in current TB therapy. With this regard, antimycobacterial peptides derived from various sources such as human cells, bacterial sources, mycobacteriophages, fungal, plant and animal sources could be considered as antituberculosis leads as most of these peptides are associated with dual advantages of having both bactericidal activity towards Mtb as well as immuno-regulatory property. Some of the peptides possess the additional advantage of interacting synergistically with antituberculosis medications too, thereby increasing their efficiency, underscoring the vigour of antimicrobial peptides (AMPs) as best possible alternative therapeutic candidates or adjuvants in TB treatment. Albeit the beneficiary features of these peptides, few obstacles allied with them like cytotoxicity and proteolytic degradation are matter of concerns too. In this review, we have focused on structural hallmarks, targeting mechanisms and specific structural aspects contributing to antimycobacterial activity and discovered natural and synthetic antimycobacterial peptides along with their sources, anti-TB, immuno-regulatory properties, merits and demerits and possible delivery methods of AMPs.

Membrane-active and DNA binding related double-action antimycobacterial mechanism of antimicrobial peptide W3R6 and its synthetic analogs

The emergence of multidrug- or extremely drug-resistant M. tuberculosis strains has made very few drugs available for current tuberculosis treatment. Antimicrobial peptides can be employed as a promising alternative strategy for TB treatment. Here, we designed and synthesized a series of peptide sequences based on the structure-activity relationships of natural sequences of antimicrobial peptides. The peptide W3R6 and its analogs were screened and found to have potent antimycobacterial activity against M. smegmatis, and no hemolytic activity against human erythrocytes. The evidence from the mechanism of action study indicated that W3R6 and its analogs can interact with the mycobacterial membrane in a lytic manner and form pores on the outer membrane of M. smegmatis. Significant colocalization of D-W3R6 with mycobacterial DNA was observed by confocal laser scanning microscopy and DNA retardation assays, which suggested that the antimycobacterial mechanism of action of the peptide was associated with the unprotected genomic DNA of M. smegmatis. In general, W3R6 and its analogs act on not only the mycobacterial membrane but also the genomic DNA in the cytoplasm, which makes it difficult for mycobacteria to generate resistance due to the peptides having two targets. In addition, the peptides can effectively eliminate M. smegmatis cells from infected macrophages. Our findings indicated that the antimicrobial peptide W3R6 could be a novel lead compound to overcome the threat from drug-resistant M. tuberculosis strains in the development of potent AMPs for TB therapeutic applications.

Characterization and genome analysis of G1 sub-cluster mycobacteriophage Lang

Phage therapy is revitalized as an alternative to antibiotics therapy against antimicrobials resistant pathogens. Mycobacteriophages are genetically diverse viruses that can specifically infect Mycobacterium genus including Mycobacterium tuberculosis and Mycobacterium smegmatis. Here, we isolated and annotated the genome of a mycobacteriophage Lang, a temperate mycobacteriophage isolated from the soil of Hohhot, Inner Mongolia, China, by using Mycolicibacterium smegmatis mc² 155 as the host. It belongs to the Siphoviridae family of Caudovirales as determined by transmission electron microscopy. The morphological characteristics and certain biological properties of the phage were considered in detail. Phage Lang genomes is 41,487 bp in length with 66.85% GC content and encodes 60 putative open reading frames and belongs to the G1 sub-cluster. Genome annotation indicated that genes for structure proteins, assembly proteins, replications/transcription and lysis of the host are present in function clucters. The genome sequence of phage Lang is more than 95% similar to that of mycobacteriophage Grizzly and Sweets, differing in substitutions, insertions and deletions in Lang. One-step growth curve revealed that Lang has a latent period of 30 min and a outbreak period of 90 min. The short latent period and rapid outbreak mark the unique properties of phage Lang, which can be another potential source for combating M. tuberculosis.

The protective action of piperlongumine against mycobacterial pulmonary tuberculosis in its mitigation of inflammation and macrophage infiltration in male BALB/c mice

Introduction

Piperlongumine (PL) is a bioactive alkaloid and medicinal compound of piperamide isolated from the long pepper (Piper longum Linn). It has demonstrated bactericidal action against Mycobacterium tuberculosis (MTB), the cause of pulmonary tuberculosis; nevertheless, immunomodulatory activity had not been identified for it in MTB-triggered granulomatous inflammation. This study investigated if piperlongumine could inhibit such inflammation.

Material and Methods

Mycobacterium tuberculosis strain H37Rv was subjected to a broth microdilution assay. Piperlongumine at 5, 15, and 25 μg/mL, 0.2% dimethyl sulphoxide as control or 4 μM of dexamethasone were tested in vitro on MH-S murine alveolar macrophages. BALB/c mice were orally administered PL at 50, 100 and 150 mg/kg b.w. after trehalose-6,6-dimycolate (TDM) stimulation. Chemokine and cytokine concentrations were determined in lung supernatants. Flow cytometry and Western blot analysis were performed to determine phosphorylated spleen tyrosine kinase (Syk), c-Jun N-terminal kinase (JNK) and extracellular signal-regulated kinase (ERK) pathways.

Results

Piperlongumine inhibited inflammatory mediators and adherence of lymphocyte function-associated antigen 1 to MH-S cells following TDM activation. It also improved macrophage clearance of MTB. In TDM-stimulated MH-S cells, PL significantly influenced the macrophage inducible Ca²⁺-dependent lectin receptor (Mincle)-Syk-ERK signalling pathway. Oral dosing of PL effectively suppressed the development of pulmonary granulomas and inflammatory reactions in the TDM-elicited mouse granuloma model.

Conclusion

PL as an inhibitor of MTB-triggered granulomatous inflammation may be an effective complementary treatment for mycobacterial infection.

Antimicrobial Peptides: An Update on Classifications and Databases

Antimicrobial peptides (AMPs) are distributed across all kingdoms of life and are an indispensable component of host defenses. They consist of predominantly short cationic peptides with a wide variety of structures and targets. Given the ever-emerging resistance of various pathogens to existing antimicrobial therapies, AMPs have recently attracted extensive interest as potential therapeutic agents. As the discovery of new AMPs has increased, many databases specializing in AMPs have been developed to collect both fundamental and pharmacological information. In this review, we summarize the sources, structures, modes of action, and classifications of AMPs. Additionally, we examine current AMP databases, compare valuable computational tools used to predict antimicrobial activity and mechanisms of action, and highlight new machine learning approaches that can be employed to improve AMP activity to combat global antimicrobial resistance.

Genomic and proteomic portrait of a novel mycobacteriophage SWU2 isolated from China

Phage therapy, especially combination with antibiotics, was revitalized to control the antibiotics resistance. Mycobacteriophage, the phage of mycobacterium with the most notorious Mycobacterium tuberculosis (M. tuberculosis), was intensively explored. A novel mycobacteriophage SWU2 was isolated from a soil sample collected at Nanchang city, Jiangxi province, China, by using Mycolicibacterium smegmatis (M. smegmatis) mc² 155 as the host. Phage morphology and biology were characterized. Phage structure proteins were analyzed by LC-MS/MS. The putative functions of phage proteins and multi-genome comparison were performed with bioinformatics. The transmission electron microscopy result indicated that this phage belongs to Siphoviridae of Caudovirales. Plaques of SWU2 appeared clear but small. In a one-step growth test, we demonstrated that SWU2 had a latent period of 30 min and a logarithmic phase of 120 min. Among the 76 predicted Open Reading Frames (ORFs), 9 ORFs were identified as phage structure proteins of SWU2. The assembled phage genome size is 50,013 bp, with 62.7% of G + C content. SWU2 genome sequence shares 88% identity with Mycobacterium phages HINdeR and Timshel, differing in substitutions, insertions and deletions in SWU2. Phylogenetic tree revealed that SWU2 is grouped into A7 sub-cluster. There are several substitutions, insertions and deletions in SWU2 genome in comparison with close cousin phages HINdeR and Timshel. The new phage adds another dimension of abundance to the mycobacteriophages.

Host-Pathogen Dialogues in Autophagy, Apoptosis, and Necrosis during Mycobacterial Infection

Mycobacterium tuberculosis (Mtb) is an etiologic pathogen of human tuberculosis (TB), a serious infectious disease with high morbidity and mortality. In addition, the threat of drug resistance in anti-TB therapy is of global concern. Despite this, it remains urgent to research for understanding the molecular nature of dynamic interactions between host and pathogens during TB infection. While Mtb evasion from phagolysosomal acidification is a well-known virulence mechanism, the molecular events to promote intracellular parasitism remains elusive. To combat intracellular Mtb infection, several defensive processes, including autophagy and apoptosis, are activated. In addition, Mtb-ingested phagocytes trigger inflammation, and undergo necrotic cell death, potentially harmful responses in case of uncontrolled pathological condition. In this review, we focus on Mtb evasion from phagosomal acidification, and Mtb interaction with host autophagy, apoptosis, and necrosis. Elucidation of the molecular dialogue will shed light on Mtb pathogenesis, host defense, and development of new paradigms of therapeutics.

Phage therapy as a renewed therapeutic approach to mycobacterial infections: a comprehensive review

Mycobacterial infections are considered to a serious challenge of medicine, and the emergence of MDR and XDR tuberculosis is a serious public health problem. Tuberculosis can cause high morbidity and mortality around the world, particularly in developing countries. The emergence of drug-resistant Mycobacterium infection following limited therapeutic technologies coupled with the serious worldwide tuberculosis epidemic has adversely affected control programs, thus necessitating the study of the role bacteriophages in the treatment of mycobacterial infection. Bacteriophages are viruses that are isolated from several ecological specimens and do not exert adverse effects on patients. Phage therapy can be considered as a significant alternative to antibiotics for treating MDR and XDR mycobacterial infections. The useful ability of bacteriophages to kill Mycobacterium spp has been explored by numerous research studies that have attempted to investigate the phage therapy as a novel therapeutic/diagnosis approach to mycobacterial infections. However, there are restricted data about phage therapy for treating mycobacterial infections. This review presents comprehensive data about phage therapy in the treatment of mycobacterial infection, specifically tuberculosis disease.

A review on anti-tuberculosis peptides: Impact of peptide structure on anti-tuberculosis activity

Antibiotic resistance is a major public health problem globally. Particularly concerning amongst drug-resistant human pathogens is Mycobacterium tuberculosis that causes the deadly infectious tuberculosis (TB) disease. Significant issues associated with current treatment options for drug-resistant TB and the high rate of mortality from the disease makes the development of novel treatment options against this pathogen an urgent need. Antimicrobial peptides are part of innate immunity in all forms of life and could provide a potential solution against drug-resistant TB. This review is a critical analysis of antimicrobial peptides that are reported to be active against the M tuberculosis complex exclusively. However, activity on non-TB strains such as Mycobacterium avium and Mycobacterium intracellulare, whenever available, have been included at appropriate sections for these anti-TB peptides. Natural and synthetic antimicrobial peptides of diverse sequences, along with their chemical structures, are presented, discussed, and correlated to their observed antimycobacterial activities. Critical analyses of the structure allied to the anti-mycobacterial activity have allowed us to draw important conclusions and ideas for research and development on these promising molecules to realise their full potential. Even though the review is focussed on peptides, we have briefly summarised the structures and potency of the various small molecule drugs that are available and under development, for TB treatment.

Bacteriophage gene products as potential antimicrobials against tuberculosis

Tuberculosis (TB) is recognised as one of the most pressing global health threats among infectious diseases. Bacteriophages are adapted for killing of their host, and they were exploited in antibacterial therapy already before the discovery of antibiotics. Antibiotics as broadly active drugs overshadowed phage therapy for a long time. However, owing to the rapid spread of antibiotic resistance and the increasing complexity of treatment of drug-resistant TB, mycobacteriophages are being studied for their antimicrobial potential. Besides phage therapy, which is the administration of live phages to infected patients, the development of drugs of phage origin is gaining interest. This path of medical research might provide us with a new pool of previously undiscovered inhibition mechanisms and molecular interactions which are also of interest in basic research of cellular processes, such as transcription. The current state of research on mycobacteriophage-derived anti-TB treatment is reviewed in comparison with inhibitors from other phages, and with focus on transcription as the host target process.

A small mycobacteriophage-derived peptide and its improved isomer restrict mycobacterial infection via dual mycobactericidal-immunoregulatory activities

Mycobacteriophages express various peptides/proteins to infect Mycobacterium tuberculosis (M. tb). Particular attention has been paid to mycobacteriophage-derived endolysin proteins. We herein characterized a small mycobacteriophage-derived peptide designated AK15 with potent anti-M. tb activity. AK15 adopted cationic amphiphilic α-helical structure, and on the basis of this structure, we designed six isomers with increased hydrophobic moment by rearranging amino acid residues of the helix. We found that one of these isomers, AK15-6, exhibits enhanced anti-mycobacterial efficiency. Both AK15 and AK15-6 directly inhibited M. tb by trehalose 6,6'-dimycolate (TDM) binding and membrane disruption. They both exhibited bactericidal activity, cell selectivity, and synergistic effects with rifampicin, and neither induced drug resistance to M. tb They efficiently attenuated mycobacterial load in the lungs of M. tb-infected mice. We observed that lysine, arginine, tryptophan, and an α-helix are key structural requirements for their direct anti-mycobacterial action. Of note, they also exhibited immunomodulatory effects, including inhibition of proinflammatory response in TDM-stimulated or M. tb-infected murine bone marrow-derived macrophages (BMDMs) and M.tb-infected mice and induction of only a modest level of cytokine (tumor necrosis factor α (TNF-α) and interleukin-6 (IL-6)) production in murine BMDMs and a T-cell cytokine (interferin-γ (IFN-γ) and TNF-α) response in murine lung and spleen. In summary, characterization of a small mycobacteriophage-derived peptide and its improved isomer revealed that both efficiently restrain M. tb infection via dual mycobactericidal-immunoregulatory activities. Our work provides clues for identifying small mycobacteriophage-derived anti-mycobacterial peptides and improving those that have cationic amphiphilic α-helices.

Tachyplesin Causes Membrane Instability That Kills Multidrug-Resistant Bacteria by Inhibiting the 3-Ketoacyl Carrier Protein Reductase FabG

Tachyplesin is a type of cationic β-hairpin antimicrobial peptide discovered in horseshoe crab approximately 30 years ago that is well known for both its potential antimicrobial activities against multidrug-resistant bacteria and its cytotoxicity to mammalian cells. Though its physical interactions with artificial membranes have been well studied, details of its physiological mechanism of action the physiological consequences of its action remain limited. By using the DNA-binding fluorescent dye propidium iodide to monitor membrane integrity, confocal microscopy to assess the intracellular location of FITC-tagged tachyplesin, and RNA sequencing of the differentially expressed genes in four Gram-negative bacteria (Escherichia coli, Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa) treated with lethal or sublethal concentrations of tachyplesin, we found that compared with levofloxacin-treated bacteria, tachyplesin-treated bacteria showed significant effects on the pathways underlying unsaturated fatty acid biosynthesis. Notably, RNA levels of the conserved and essential 3-ketoacyl carrier protein reductase in this pathway (gene FabG) were elevated in all of the four bacteria after tachyplesin treatment. In vitro tests including surface plasmon resonance and enzyme activity assays showed that tachyplesin could bind and inhibit 3-ketoacyl carrier protein reductase, which was consistent with molecular docking prediction results. As unsaturated fatty acids are important for membrane fluidity, our results provided one possible mechanism to explain how tachyplesin kills bacteria and causes cytotoxicity by targeting membranes, which may be helpful for designing more specific and safer antibiotics based on the function of tachyplesin.

Sophora flavescens protects against mycobacterial Trehalose Dimycolate-induced lung granuloma by inhibiting inflammation and infiltration of macrophages

The immune system responds to Mycobacterium tuberculosis (MTB) infection by forming granulomas to quarantine the bacteria from spreading. Granuloma-mediated inflammation is a cause of lung destruction and disease transmission. Sophora flavescens (SF) has been demonstrated to exhibit bactericidal activities against MTB. However, its immune modulatory activities on MTB-mediated granulomatous inflammation have not been reported. In the present study, we found that flavonoids from Sophora flavescens (FSF) significantly suppressed the pro-inflammatory mediators released from mouse lung alveolar macrophages (MH-S) upon stimulation by trehalose dimycolate (TDM), the most abundant lipoglycan on MTB surface. Moreover, FSF reduced adhesion molecule (LFA-1) expression on MH-S cells after TDM stimulation. Furthermore, FSF treatment on TDM-activated lung epithelial (MLE-12) cells significantly downregulated macrophage chemoattractant protein (MCP-1/CCL2) expression, which in turn reduced the in vitro migration of MH-S to MLE-12 cells. In addition, FSF increased the clearance of mycobacterium bacteria (Mycobacterium aurum) in macrophages. FSF mainly affected the Mincle-Syk-Erk signaling pathway in TDM-activated MH-S cells. In TDM-induced mouse granulomas model, oral administration with FSF significantly suppressed lung granulomas formation and inflammation. These findings collectively implicated an anti-inflammatory role of FSF on MTB-mediated granulomatous inflammation, thereby providing evidence of FSF as an efficacious adjunct treatment during mycobacterial infection.