Rational Design of Hybrid Peptides: A Novel Drug Design Approach

Design and bioactivity evaluation of a novel autotaxin inhibitor with anti-hepatic fibrosis effects

Autotaxin (ATX) is considered as a serum marker of hepatic fibrosis, which is positively correlated with the degree of hepatic fibrosis. However, there are no clinical studies on anti-hepatic fibrosis drugs targeting ATX. This study attempts to find novel ATX small molecule inhibitors based on virtual screening methods including two-dimensional similarity search, pharmacophore screening, molecular docking, drug-like properties and ADMET filtration, combined with biological evaluation. An ATX inhibitor (IC50 = 43.05 µmol/L) is discovered by our screening strategy. In vivo result show that the novel ATX inhibitor represents excellent anti-hepatic fibrosis effects in mice. This screening strategy had potential significance for the discovery of ATX inhibitors in the future.

Antimicrobial and anti-inflammatory effects of antimicrobial peptide Lf-KR against carbapenem-resistant Escherichia coli

BACKGROUND

Carbapenem-resistant Escherichia coli (CREC) is one of the most significant clinical pathogens, primarily emerging owing to the widespread use of broad-spectrum antibiotics. Antimicrobial resistance is a major global health challenge that prolongs treatment duration and increases healthcare costs. This study evaluated the antibacterial and anti-inflammatory effects of the antimicrobial peptide Lf-KR against CREC.

METHODS

Broth microdilution method, growth curve analysis, and time-kill assays were performed to evaluate the antibacterial activity of Lf-KR against CREC. The working mechanism of Lf-KR was elucidated using N-phenyl-1-naphthylamine, propidium iodide fluorochrome, and lipopolysaccharide-binding assays. qRT-PCR was used to assess the peptide's effects on the expression of pro-inflammatory cytokines expression during infection. Furthermore, the safety and stability of Lf-KR were assessed by testing its cytotoxicity, hemolytic activity, and antibacterial stability under various conditions. The Galleria mellonella infection model was applied to evaluate the in vivo activity of Lf-KR.

RESULTS

In vitro tests showed that Lf-KR exhibited potent antibacterial activity against CREC, with the minimum inhibitory concentrations of ranging from 4-8 µg/mL and minimum bactericidal concentrations 4-16 µg/mL. Mechanistically, Lf-KR induced bacterial cell death by disrupting the bacterial membrane. Furthermore, Lf-KR significantly reduced the expression of pro-inflammatory cytokine genes, including IL-1β, IL-6, and TNF-α, in RAW 264.7 macrophage cells infected with CREC. Lf-KR concentrations < 128 µg/mL showed no significant cytotoxicity or erythrocyte hemolytic activity. Lf-KR antibacterial activity was stable across a wide temperature range (- 80 °C to 65 °C), although it was more susceptible to inhibition by fetal bovine serum. The G. mellonella infection model further demonstrated the robust antimicrobial activity of Lf-KR.

CONCLUSIONS

This study demonstrated that the antimicrobial peptide Lf-KR is a highly promising antimicrobial and anti-inflammatory agent against CREC, with potential applications in combating multi drug-resistant bacterial infections.

The de novo strategy for bifunctional peptides coating to enhance osteointegration capacity of the implant

Bone implants represent a significant global market; however, they are plagued by a high long-term failure rate, with approximately 19.2 % of implants failing within 10 years. This leads to considerable physical pain, mental distress for patients, and a substantial financial burden on public healthcare systems. Herein, we propose a novel strategy that using the interactions between positively charged hexa-arginine (R6) and polyphenols in EGC/Fe MPN to present the bifunctional peptides, cellular adhesive peptide (RGD) and osteogenic growth peptide (OGP), onto implant coatings. To thoroughly investigate the preparation process and the physical and chemical properties of the dual-peptide functionalized coatings, several techniques were employed, including dissipation-quartz crystal microbalance (DQCM), ellipsometry, photoelectron spectroscopy (XPS), and atomic force microscopy (AFM). These methods provided insights into the coating's composition, stability, mechanical properties, and surface roughness. In comparison to single-peptide functionalized coatings, the dual-peptide coatings demonstrated significantly improved performance in cellular adhesion at early stages, long-term cell proliferation, migration, antioxidant activity, osteogenic differentiation, inhibition of osteoclastogenesis, and enhanced in vivo osteointegration. This study contributes to the development of multifunctional coatings tailored to the complex biological processes involved in osteointegration.

Trends in the research and development of peptide drug conjugates: artificial intelligence aided design

Peptide-drug conjugates (PDCs) represent an emerging class of targeted therapeutic agents that consist of small molecular drugs coupled to multifunctional peptides through cleavable or non-cleavable linkers. The principal advantage of PDCs lies in their capacity to deliver drugs to diseased tissues at increased local concentrations, thereby reducing toxicity and mitigating adverse effects by limiting damage to non-diseased tissues. Despite the increasing number of PDCs being developed for various diseases, their advancements remain relatively slow due to several development constraints, which include limited available peptides and linkers, narrow therapeutic applications, and incomplete evaluation and information platforms for PDCs. Marked by the recent Nobel Prize awarded to artificial intelligence (AI) and de novo protein design for "protein design and structure prediction," AI is playing an increasingly important role in drug discovery and development. In this review, we summarize the recent developments and limitations of PDCs, highlights the potential of AI in revolutionizing the design and evaluation of PDC.

A review on pyrimidine-based pharmacophore as a template for the development of hybrid drugs with anticancer potential

The low efficacy and toxicity of traditional chemotherapy, led by drug resistance of targeted anticancer therapies, have mandated the exploration and development of anticancer molecules. In this league, hybrid drugs, owing to their peculiar multitargeted functionality and structural diversity, could serve as vital leads in this quest for drug discovery. They are plausibly found to offer added advantages considering the improved efficacy, low toxicity, and improved patient compliance. Among numerous heterocycles explored, pyrimidine derivatives epitomize as a valuable resource for the hybrid drug development due to their validated efficacy and versatility. The present review discusses the role of pyrimidine, a diversified pharmacophore in drug development and concepts of hybrid drugs. The study covers the recent advancements in pyrimidine-based hybrid pharmacophores. It delves further into the challenges in hybrid drug development and ongoing research in hybrid drug discovery. Furthermore, the challenges faced in developing hybrid molecules, such as their design and optimization complexities, bioavailability and pharmacokinetics issues, target identification and validation, and off-target effects, are discussed.

Antimicrobial Peptides and Their Mimetics: Promising Candidates of Next-Generation Therapeutic Agents Combating Multidrug-Resistant Bacteria

The increasing morbidity and mortality caused by multidrug-resistant bacteria alerts human beings to the fact that conventional antibiotics are no longer reliable and effective alternatives are imperatively needed. Owing to wide range of sources, diverse structures, and unique mode of action, antimicrobial peptides have been highly anticipated and extensively studied in recent years. Besides, the integration of artificial intelligence helps researchers gain access to the vast unexplored chemical space, which opens more opportunities for the optimization and design of novel structures. Moreover, Due to advances in chemistry and synthetic biology, researchers have also begun to focus on the potential of chemical mimetics of antimicrobial peptides. In this review, a comprehensive discussion about natural and synthesized antimicrobial peptides as well as their chemical mimetics is made, so as to provide a comprehensive summary of this field and inspire follow-up research.

Advances in Artificially Designed Antibacterial Active Antimicrobial Peptides

Antibacterial resistance has emerged as a significant global concern, necessitating the urgent development of new antibacterial drugs. Antimicrobial peptides (AMPs) are naturally occurring peptides found in various organisms. Coupled with a wide range of antibacterial activity, AMPs are less likely to develop drug resistance and can act as potential agents for treating bacterial infections. However, their characteristics, such as low activity, instability, and toxicity, hinder their clinical application. Consequently, researchers are inclined towards artificial design and optimization based on natural AMPs. This review discusses the research advancements in the field of artificial designing and optimization of various AMPs. Moreover, it highlights various strategies for designing such peptides, aiming to provide valuable insights for developing novel AMPs.

A Review of Antimicrobial Peptides: Structure, Mechanism of Action, and Molecular Optimization Strategies

Antimicrobial peptides (AMPs) are bioactive macromolecules that exhibit antibacterial, antiviral, and immunomodulatory functions. They come from a wide range of sources and are found in all forms of life, from bacteria to plants, vertebrates, and invertebrates, and play an important role in controlling the spread of pathogens, promoting wound healing and treating tumors. Consequently, AMPs have emerged as promising alternatives to next-generation antibiotics. With advancements in systems biology and synthetic biology technologies, it has become possible to synthesize AMPs artificially. We can better understand their functional activities for further modification and development by investigating the mechanism of action underlying their antimicrobial properties. This review focuses on the structural aspects of AMPs while highlighting their significance for biological activity. Furthermore, it elucidates the membrane targeting mechanism and intracellular targets of these peptides while summarizing molecular modification approaches aimed at enhancing their antibacterial efficacy. Finally, this article outlines future challenges in the functional development of AMPs along with proposed strategies to overcome them.

Dehydroabietylamine-substituted trifluorobenzene sulfonamide rhodamine B hybrids as anticancer agents overcoming drug resistance

Attachment of a conjugate assembled from a novel fluorinated carbonic anhydrase inhibitor and rhodamine B onto dehydroabietylamine (DHA) or cyclododecylamine led to first-in-class conjugates of good cytotoxicity; thereby IC50 values (from SRB assays; employed tumor cell lines A2780, A2780Cis, A549, HT29, MCF7, and non-malignant human fibroblasts CCD18Co) between 0.2 and 0.7 μM were found. Both conjugates showed similar cytotoxic activity but the dehydroabietylamine derived conjugate outperformed its cyclododecyl analog in terms of tumor cell/non-tumor cell selectivity. Both conjugates accumulate intracellular, and the DHA conjugate was able to overcome drug resistance which is effective independent of the expression status of carbonic anhydrase IX.

Molecular Trojan Horses for treating lysosomal storage diseases

Lysosomal storage diseases (LSDs) are caused by monogenic mutations in genes encoding for proteins related to the lysosomal function. Lysosome plays critical roles in molecule degradation and cell signaling through interplay with many other cell organelles, such as mitochondria, endoplasmic reticulum, and peroxisomes. Even though several strategies (i.e., protein replacement and gene therapy) have been attempted for LSDs with promising results, there are still some challenges when hard-to-treat tissues such as bone (i.e., cartilages, ligaments, meniscus, etc.), the central nervous system (mostly neurons), and the eye (i.e., cornea, retina) are affected. Consistently, searching for novel strategies to reach those tissues remains a priority. Molecular Trojan Horses have been well-recognized as a potential alternative in several pathological scenarios for drug delivery, including LSDs. Even though molecular Trojan Horses refer to genetically engineered proteins to overcome the blood-brain barrier, such strategy can be extended to strategies able to transport and deliver drugs to specific tissues or cells using cell-penetrating peptides, monoclonal antibodies, vesicles, extracellular vesicles, and patient-derived cells. Only some of those platforms have been attempted in LSDs. In this paper, we review the most recent efforts to develop molecular Trojan Horses and discuss how this strategy could be implemented to enhance the current efficacy of strategies such as protein replacement and gene therapy in the context of LSDs.

Rational design of hybrid peptide with high antimicrobial property derived from Melittin and Lasioglossin

Hybridization of Antimicrobial peptides (AMPs) with unique abilities is now considered to improve AMPs' function as promising therapeutic candidates. In the current research, Lasioglossin (LL-III) with a high antimicrobial effect on Acinetobacter (A.) baumanni and Melittin with a high antimicrobial effect against Staphylococcus (S.) aureus were selected for designing a hybrid peptide with modified properties. In the present study, a hybrid peptide with modified properties was designed. Molecular dynamic (MD) and coarse-grained (CG) simulations were done to evaluate the stability and interaction of the hybrid peptide with related membrane models. In this study, a truncated Melittin peptide (11 amino acids) was fused to an LL-III peptide (15 amino acids) to raise the antimicrobial activity. A new hybrid peptide analog (LM1) was selected by replacing the arginine with isoleucine in the fifth position of truncated Melittin to raise the antimicrobial rate of the peptide. The potential for binding of the LM1 to lipid membrane (D factor) was increased from 2.02 related to Melittin to 3.62. Based on VMD results, the N-terminal of LM1 peptide related to LL-III was the alpha helix during 200 ns. However, the C-terminal region related to the Melittin peptide only at 50 ns was in alpha helix form. The RMSD of the LM1 peptide was in the range of 0.2 to 0.8, which, after 160 ns, reached stability. RMSD and RMSF results indicated no unwanted fluctuations during the 200 ns MD simulation. A significant movement of LM1 peptide inside the S. aureus membrane(4.76 nm) and A. baumanni membrane (3.2 nm) was observed by CG simulation. Our findings highlight the high stability of the designed hybrid peptide and its antimicrobial potential to halter A. baumanii and S. aureus bacteria.Communicated by Ramaswamy H. Sarma.

Anti-parasitic activity of a chimeric peptide Cecropin A (2-8)-Melittin (6-9) (CM11) against tachyzoites of Toxoplasma gondii and the BALB/c mouse model of acute toxoplasmosis

Toxoplasmosis is a zoonotic disease that infects most animals, including humans. Pyrimethamine/sulfadiazine is the standard treatment for toxoplasmosis. Although this treatment has been successful, it is often associated with side effects that cannot be tolerated. Therefore, various compounds have been proposed as alternative treatments for toxoplasmosis. Antimicrobial peptides (AMPs) act on various pathogens, from viruses to protozoa. The purpose of the present study was to evaluate the effects of CM11 on in vitro and in vivo Toxoplasma gondii infection. For in vitro experiments, VERO cells were treated with different concentrations of CM11 (1-128 μg/ml) compared to sulfadiazine (SDZ) (0.78-100 μg/ml). MTT and lactate dehydrogenase (LDH) assays evaluated the cell viability and plasma membrane integrity. Then, the inhibitory concentration (IC50) values were determined for treating tachyzoites of T. gondii before or on cells previously infected. Annexin V-FITC/propidium iodide (PI) staining was used to distinguish viable and apoptotic cells. The effect of CM11, SDZ, and a combination of CM11 and SDZ was evaluated in the BALB/c mouse model of acute toxoplasmosis. CM11 was effective on tachyzoites of T. gondii and had a time and dose-dependent manner. The results of the MTT assay showed that the CC50 values of CM11 and SDZ were estimated at 17.4 µg/ml and 62.3 µg/ml after 24-h, respectively. The inhibitory concentration (IC50) of CM11 and SDZ on infected cells was estimated at 1.9 µg/ml and 1.4 µg/ml after 24-h, respectively. The highest rate of apoptosis (early and late) in high concentrations of SDZ and CM11 was determined for tachyzoites (2.13 % and 13.88 %), non-infected VERO cells (6.1 % and 19.76 %), and infected VERO cells (7.45 % and 29.9 %), respectively. Treating infected mice with CM11 and a combination of CM11 and SDZ had increased survival time. Based on the mentioned results, it can be concluded that CM11 has a beneficial effect on tachyzoites of T. gondii in vitro. The result of the mouse model suggests that CM11, either alone or in combination with other chemotherapeutic agents, could be a potential therapeutic for toxoplasmosis. Hence, antimicrobial peptides could be applied as promising anti-toxoplasma agents for treating toxoplasmosis.

A combination of a cell penetrating peptide and a protein translation inhibitor kills metastatic breast cancer cells

Cell Penetrating Peptides (CPPs) are promising anticancer and antimicrobial drugs. We recently reported that a peptide derived from the human mitochondrial/ER membrane-anchored NEET protein, Nutrient Autophagy Factor 1 (NAF-1; NAF-144-67), selectively permeates and kills human metastatic epithelial breast cancer cells (MDA-MB-231), but not control epithelial cells. As cancer cells alter their phenotype during growth and metastasis, we tested whether NAF-144-67 would also be efficient in killing other human epithelial breast cancer cells that may have a different phenotype. Here we report that NAF-144-67 is efficient in killing BT-549, Hs 578T, MDA-MB-436, and MDA-MB-453 breast cancer cells, but that MDA-MB-157 cells are resistant to it. Upon closer examination, we found that MDA-MB-157 cells display a high content of intracellular vesicles and cellular protrusions, compared to MDA-MB-231 cells, that could protect them from NAF-144-67. Inhibiting the formation of intracellular vesicles and dynamics of cellular protrusions of MDA-MB-157 cells, using a protein translation inhibitor (the antibiotic Cycloheximide), rendered these cells highly susceptible to NAF-144-67, suggesting that under certain conditions, the killing effect of CPPs could be augmented when they are applied in combination with an antibiotic or chemotherapy agent. These findings could prove important for the treatment of metastatic cancers with CPPs and/or treatment combinations that include CPPs.

Broad-spectrum hybrid antimicrobial peptides derived from PMAP-23 with potential LPS binding ability

Antimicrobial peptides, as an integral part of the innate immune system, kill bacteria through a special mechanism of action, making them less susceptible to drug resistance. However, Lipopolysaccharide (LPS) as the permeation barrier on the bacterial membrane, inhibits the antibacterial activity of antimicrobial peptides and triggers the inflammatory response. GWKRKRFG is an LPS binding sequence with a β-boomerang motif that can be linked to antimicrobial peptides to enhance their LPS affinity and reduce the possibility of LPS-induced inflammatory responses. In this study, a series of hybrid peptides were designed by conjugating the reported LPS binding sequence to the C-/N-terminal sequences of the natural porcine antimicrobial peptide PMAP-23 to increase the LPS affinity of peptides. Among all the designed hybrid peptides, 4R-PP-G8 showed the best antibacterial activity, nonhemolytic activity, and excellent cell selectivity. The presence of LPS not only induced the secondary structure transformation of 4R-PP-G8 from a random structure to an α-helical structure but also reduced the antibacterial activity of 4R-PP-G8 in a dose-dependent manner, indicating the excellent binding ability of 4R-PP-G8 to LPS. The LPS/LTA binding assay further verified the interaction between the peptide and LPS. The membrane permeability test verified that 4R-PP-G8 possessed a strong capability to penetrate the bacterial membrane after interacting with LPS. More direct membrane disruption was observed under FE-SEM and TEM. In conclusion, we provided a simple and efficient method to improve the LPS binding ability of antimicrobial peptides and enhance their antimicrobial activity, resulting in the peptide 4R-PP-G8 with clinical application potential.

Unnatural amino acids: promising implications for the development of new antimicrobial peptides

The increasing incidence and rapid spread of bacterial resistance to conventional antibiotics are a serious global threat to public health, highlighting the need to develop new antimicrobial alternatives. Antimicrobial peptides (AMPs) represent a class of promising natural antibiotic candidates due to their broad-spectrum activity and low tendency to induce resistance. However, the development of AMPs for medical use is hampered by several obstacles, such as moderate activity, lability to proteolytic degradation, and low bioavailability. To date, many researchers have focussed on the optimization or design of novel artificial AMPs with desired properties. Unnatural amino acids (UAAs) are valuable building blocks in the manufacture of a variety of pharmaceuticals, and have been used to develop artificial AMPs with specific structural and physicochemical properties. Rational incorporation of UAAs has become a very promising approach to endow AMPs with strong and long-lasting activity but no toxicity. This review aims to summarize key approaches that have been used to incorporate UAAs to develop novel AMPs with improved properties and better performance. It is anticipated that this review will guide future design considerations for UAA-based antimicrobial applications.

Engineering Approaches for the Development of Antimicrobial Peptide-Based Antibiotics

Antimicrobial peptides (AMPs) have received increasing attention as potential alternatives for future antibiotics because of the rise of multidrug-resistant (MDR) bacteria. AMPs are small cationic peptides with broad-spectrum antibiotic activities and different action mechanisms to those of traditional antibiotics. Despite the desirable advantages of developing peptide-based antimicrobial agents, the clinical applications of AMPs are still limited because of their enzymatic degradation, toxicity, and selectivity. In this review, structural modifications, such as amino acid substitution, stapling, cyclization of peptides, and hybrid AMPs with conventional antibiotics or other peptides, will be presented. Additionally, nanodelivery systems using metals or lipids to deliver AMPs will be discussed based on the structural properties and action mechanisms of AMPs.

Advances in hybrid peptide-based self-assembly systems and their applications

Self-assembly of peptides demonstrates a great potential for designing highly ordered, finely tailored supramolecular arrangements enriched with high specificity, improved efficacy and biological activity. Along with natural peptides, hybrid peptide systems composed of natural and chemically diverse unnatural amino acids have been used in various fields, including drug delivery, wound healing, potent inhibition of diseases, and prevention of biomaterial related diseases to name a few. In this review, we provide a brief outline of various methods that have been utilized for obtaining fascinating structures that create an avenue to reproduce a range of functions resulting from these folds. An overview of different self-assembled structures as well as their applications will also be provided. We believe that this review is very relevant to the current scenario and will cover conformations of hybrid peptides and resulting self-assemblies from the late 20^th century through 2022. This review aims to be a comprehensive and reliable account of the hybrid peptide-based self-assembly owing to its enormous influence in understanding and mimicking biological processes.

Nisin Variants Generated by Protein Engineering and Their Properties

Nisin, a typical lantibiotic, has robust antimicrobial activity combined with limited cytotoxicity, and the development of resistance to it is slow. These properties make nisin a promising antimicrobial agent to control pathogenic microorganisms in dairy foods. However, its low solubility, poor stability and short half-life at neutral pH limit its application within the dairy industry. Protein engineering technology has revealed the potential of modifying nisin to improve its properties, and many valuable variants have emerged. This review summarizes progress in the generation of nisin variants for the dairy industry and for other purposes. These nisin variants with additional modification have improved properties and can even expand the inhibition spectrum range of nisin. Nisin, as the most thoroughly studied lantibiotic, and its variants can also guide the modification of other lantibiotics.

Peptide Conjugates Derived from flg15, Pep13, and PIP1 That Are Active against Plant-Pathogenic Bacteria and Trigger Plant Defense Responses

Thirty peptide conjugates were designed by combining an antimicrobial peptide (BP16, BP100, BP143, KSL-W, BP387, or BP475) at the N- or C-terminus of a plant defense elicitor peptide (flg15, BP13, Pep13, or PIP1). These conjugates were highly active in vitro against six plant-pathogenic bacteria, especially against Xanthomonas arboricola pv. pruni, Xanthomonas fragariae and Xanthomonas axonopodis pv. vesicatoria. The most active peptides were those incorporating Pep13. The order of the conjugation influenced the antibacterial activity and the hemolysis. Regarding the former, peptide conjugates incorporating the elicitor peptide flg15 or Pep13 at the C-terminus were, in general, more active against Pseudomonas syringae pv. actinidiae and P. syringae pv. syringae, whereas those bearing these elicitor peptides at the N-terminus displayed higher activity against Erwinia. amylovora and the Xanthomonas species. The best peptide conjugates displayed MIC values between 0.8 and 12.5 μM against all the bacteria tested and also had low levels of hemolysis and low phytotoxicity. Analysis of the structural and physicochemical parameters revealed that a positive charge ranging from +5 to +7 and a moderate hydrophobic moment/amphipathic character is required for an optimal biological profile. Interestingly, flg15-BP475 exhibited a dual activity, causing the upregulation of the same genes as flg15 and reducing the severity of bacterial spot in tomato plants with a similar or even higher efficacy than copper oxychloride. Characterization by nuclear magnetic resonance (NMR) of the secondary structure of flg15-BP475 showed that residues 10 to 25 fold into an α-helix. This study establishes trends to design new bifunctional peptides useful against plant diseases caused by plant-pathogenic bacteria.

IMPORTANCE The consequences of plant pathogens on crop production together with the lack of effective and environmentally friendly pesticides evidence the need of new agents to control plant diseases. Antimicrobial and plant defense elicitor peptides have emerged as good candidates to tackle this problem. This study focused on combining these two types of peptides into a single conjugate with the aim to potentiate the activity of the individual fragments. Differences in the biological activity of the resulting peptide conjugates were obtained depending on their charge, amphipathicity, and hydrophobicity, as well as on the order of the conjugation of the monomers. This work provided bifunctional peptide conjugates able to inhibit several plant-pathogenic bacteria, to stimulate plant defense responses, and to reduce the severity of bacterial spot in tomato plants. Thus, this study could serve as the basis for the development of new antibacterial/plant defense elicitor peptides to control bacterial plant pathogens.

Modeling the MreB-CbtA Interaction to Facilitate the Prediction and Design of Candidate Antibacterial Peptides

Protein-protein interactions (PPIs) have emerged as promising targets for PPI modulators as alternative drugs because they are essential for most biochemical processes in living organisms. In recent years, a spotlight has been put on the development of peptide-based PPI inhibitors as the next-generation therapeutics to combat antimicrobial resistance taking cognizance of protein-based PPI-modulators that interact with target proteins to inhibit function. Although protein-based PPI inhibitors are not effective therapeutic agents because of their high molecular weights, they could serve as sources for peptide-based pharmaceutics if the target-inhibitor complex is accessible and well characterized. The Escherichia coli (E. coli) toxin protein, CbtA, has been identified as a protein-based PPI modulator that binds to the bacterial actin homolog MreB leading to the perturbation of its polymerization dynamics; and consequently has been suggested to have antibacterial properties. Unfortunately, however, the three-dimensional structures of CbtA and the MreB-CbtA complex are currently not available to facilitate the optimization process of the pharmacological properties of CbtA. In this study, computer modeling strategies were used to predict key MreB-CbtA interactions to facilitate the design of antiMreB peptide candidates. A model of the E. coli CbtA was built using the trRosetta software and its stability was assessed through molecular dynamics (MD) simulations. The modeling and simulations data pointed to a model with reasonable quality and stability. Also, the HADDOCK software was used to predict a possible MreB-CbtA complex, which was characterized through MD simulations and compared with MreB-MreB dimmer. The results suggest that CbtA inhibits MreB through the competitive mechanism whereby CbtA competes with MreB monomers for the interprotofilament interface leading to interference with double protofilament formation. Additionally, by using the antiBP software to predict antibacterial peptides in CbtA, and the MreB-CbtA complex as the reference structure to determine important interactions and contacts, candidate antiMreB peptides were suggested. The peptide sequences could be useful in a rational antimicrobial peptide hybridization strategy to design novel antibiotics. All-inclusive, the data reveal the molecular basis of MreB inhibition by CbtA and can be incorporated in the design/development of the next-generation antibacterial peptides targeting MreB.

Antimicrobial peptides: mechanism of action, activity and clinical potential

The management of bacterial infections is becoming a major clinical challenge due to the rapid evolution of antibiotic resistant bacteria. As an excellent candidate to overcome antibiotic resistance, antimicrobial peptides (AMPs) that are produced from the synthetic and natural sources demonstrate a broad-spectrum antimicrobial activity with the high specificity and low toxicity. These peptides possess distinctive structures and functions by employing sophisticated mechanisms of action. This comprehensive review provides a broad overview of AMPs from the origin, structural characteristics, mechanisms of action, biological activities to clinical applications. We finally discuss the strategies to optimize and develop AMP-based treatment as the potential antimicrobial and anticancer therapeutics.

A Bifunctional Peptide Conjugate That Controls Infections of Erwinia amylovora in Pear Plants

In this paper, peptide conjugates were designed and synthesized by incorporating the antimicrobial undecapeptide BP16 at the C- or N-terminus of the plant defense elicitor peptide flg15, leading to BP358 and BP359, respectively. The evaluation of their in vitro activity against six plant pathogenic bacteria revealed that BP358 displayed MIC values between 1.6 and 12.5 μM, being more active than flg15, BP16, BP359, and an equimolar mixture of BP16 and flg15. Moreover, BP358 was neither hemolytic nor toxic to tobacco leaves. BP358 triggered the overexpression of 6 out of the 11 plant defense-related genes tested. Interestingly, BP358 inhibited Erwinia amylovora infections in pear plants, showing slightly higher efficacy than the mixture of BP16 and flg15, and both treatments were as effective as the antibiotic kasugamycin. Thus, the bifunctional peptide conjugate BP358 is a promising agent to control fire blight and possibly other plant bacterial diseases.

A Systematic Screening of Traditional Chinese Medicine Identifies Two Novel Inhibitors Against the Cytotoxic Aggregation of Amyloid Beta

The toxic aggregates of amyloid beta (Aβ) disrupt the cell membrane, induce oxidative stress and mitochondrial dysfunction, and eventually lead to Alzheimer’s disease (AD). Intervening with this cytotoxic aggregation process has been suggested as a potential therapeutic approach for AD and other protein misfolding diseases. Traditional Chinese Medicine (TCM) has been used to treat AD and related cognitive impairment for centuries with obvious efficacy. Extracts or active ingredients of TCMs have been reported to inhibit the aggregation and cytotoxicity of Aβ. However, there is a lack of systematic research on the anti-Aβ aggregation effects of TCM components. In this study, we performed a systematic screening to identify the active ingredients of TCM against the cytotoxic aggregation of Aβ42. Through a literature and database survey, we selected 19 TCM herbals frequently used in the treatment of AD, from which 76 major active chemicals without known anti-amyloid effects were further screened. This took place through two rounds of MTT-based screening detection of the cytotoxicity of these chemicals and their effects on Aβ42-induced cytotoxicity, respectively. Tetrahydroxystilbene-2-O-β-D-glucoside (TSG) and sinapic acid (SA) were found to be less toxic, and they inhibited the cytotoxicity of Aβ42. Further studies demonstrated that TSG and SA concentration-dependently attenuated the amyloidosis and membrane disruption ability of Aβ42. Thus, we identified two novel chemicals (TSG and SA) against the cytotoxic aggregation of Aβ42. Nonetheless, further exploration of their therapeutic potential is warranted.

Nano-based approaches in the development of antiviral agents and vaccines

Outbreaks and the rapid transmission of viruses, such as coronaviruses and influenza viruses, are serious threats to human health. A major challenge in combating infectious diseases caused by viruses is the lack of effective methods for prevention and treatment. Nanotechnology has provided a basis for the development of novel antiviral strategies. Owing to their large modifiable surfaces that can be functionalized with multiple molecules to realize sophisticated designs, nanomaterials have been developed as nanodrugs, nanocarriers, and nano-based vaccines to effectively induce sufficient immunologic memory. From this perspective, we introduce various nanomaterials with diverse antiviral mechanisms and summarize how nano-based antiviral agents protect against viral infection at the molecular, cellular, and organismal levels. We summarize the applications of nanomaterials for defense against emerging viruses by trapping and inactivating viruses and inhibiting viral entry and replication. We also discuss recent progress in nano-based vaccines with a focus on the mechanisms by which nanomaterials contribute to immunogenicity. We further describe how nanotechnology may improve vaccine efficacy by delivering large amounts of antigens to target immune cells and enhancing the immune response by mimicking viral structures and activating dendritic cells. Finally, we provide an overview of future prospects for nano-based antiviral agents and vaccines.

Anti-Staphylococcal and cytotoxic activities of the short anti-microbial peptide PVP

Over the past years, short anti-microbial peptides have drawn growing attention in the research and trade literature because they are usually capable of killing a broad spectrum of pathogens by employing unique mechanisms of action. This study aimed to evaluate the anti-bacterial effects of a previously designed peptide named PVP towards the clinical strains of methicillin-resistant Staphylococcus aureus (MRSA) in vitro. Secondary structure, cytotoxicity, and membrane-permeabilizing effects of the peptide were also assessed. PVP had a tendency to adopt alpha-helical conformation based upon structural predictions and circular dichroism spectroscopy (in 50% trifluoroethanol). The peptide showed MIC values ranging from 1 to 16 µg/mL against 10 strains of MRSA. In contrast to ciprofloxacin and gentamicin, PVP at sub-lethal concentration (1 µg/mL) did not provoke the development of peptide resistance after 14 serial passages. Remarkably, 1 h of exposure to 4 × MBC of PVP (8 µg/mL) was sufficient for total bacterial clearance, whereas 4 × MBC of vancomycin (8 µg/mL) failed to totally eradicate bacterial cells, even after 8 h. PVP showed negligible cytotoxicity against human dermal fibroblasts at concentrations required to kill the MRSA strains. The results of flow cytometric analysis and fluorescence microscopy revealed that PVP caused bacterial membrane permeabilization, eventually culminating in cell death. Owing to the potent anti-bacterial activity, fast bactericidal kinetics, and negligible cytotoxicity, PVP has the potential to be used as a candidate antibiotic for the topical treatment of MRSA infections.

Figainin 1, a Novel Amphibian Skin Peptide with Antimicrobial and Antiproliferative Properties

Amphibian skin secretions are abundant in bioactive compounds, especially antimicrobial peptides. These molecules are generally cationic and rich in hydrophobic amino acids, have an amphipathic structure and adopt an α-helical conformation when in contact with microorganisms membranes. In this work, we purified and characterized Figainin 1, a novel antimicrobial and antiproliferative peptide from the cutaneous secretion of the frog Boana raniceps. Figainin 1 is a cationic peptide with eighteen amino acid residues—rich in leucine and isoleucine, with an amidated C-terminus—and adopts an α-helical conformation in the presence of trifluoroethanol (TFE). It displayed activity against Gram-negative and especially Gram-positive bacteria, with MIC values ranging from 2 to 16 µM, and showed an IC₅₀ value of 15.9 µM against epimastigote forms of T. cruzi; however, Figanin 1 did not show activity against Candida species. This peptide also showed cytolytic effects against human erythrocytes with an HC₅₀ of 10 µM, in addition to antiproliferative activity against cancer cells and murine fibroblasts, with IC₅₀ values ranging from 10.5 to 13.7 µM. Despite its adverse effects on noncancerous cells, Figainin 1 exhibits interesting properties for the development of new anticancer agents and anti-infective drugs against pathogenic microorganisms.

Red Iberoamericana para el desarrollo de péptidos terapéuticos, REDIPEPT

En este contexto nace REDIPEPT, la Red Iberoamericana de Péptidos Terapéuticos, cuyo objetivo fundamental es crear y fortalecer vínculos de colaboración entre grupos iberoamericanos que desarrollan investigación focalizada en la búsqueda, identificación, diseño y síntesis de péptidos y derivados con potencial terapéutico. Los temas de investigación de interés general incluyen síntesis de péptidos de potencial actividad biológica, el aislamiento y la caracterización de nuevos productos, estudios de la relación estructura-actividad, la diversidad molecular, el diseño de novo, la administración de fármacos y el descubrimiento de nuevos agentes farmacéuticos. Para ello, se generarán Plataformas que incorporen y compartan las fortalezas de los grupos que formen parte de la red, en el diseño y la síntesis de péptidos, así como en la determinación del potencial biológico de estos. Las dianas de interés serán aquellas enfermedades de alto impacto en la salud de los países que conforman la red, con énfasis en enfermedades infecciosas de carácter bacterial o viral (Covid-19, Dengue, Zica, Chikungunya, Chagas, Tuberculosis, entre otras), degenerativas como el Alzheimer, o catastróficas como el cáncer.

Copper and iron ions accelerate the prion-like propagation of α-synuclein: A vicious cycle in Parkinson's disease

Protein fibrils drive the onset and progression of many diseases in a prion-like manner, i.e. they transcellular propagate through the extracellular space to health cells to initiate toxic aggregation as seeds. The conversion of native α-synuclein into filamentous aggregates in Lewy bodies is a hallmark of Parkinson's disease (PD). Copper and iron ions accumulate in PD brains, however, whether they influence the prion-like propagation of α-synuclein remain unclear. Here, we reported that copper/iron ions accelerate prion-like propagation of α-synuclein fibrils by promoting cellular internalization of α-synuclein fibrils, intracellular α-synuclein aggregation and the subsequent release of mature fibrils to the extracellular space to induce further propagation. Mechanistically, copper/iron ions enhanced α-synuclein fibrils internalization was mediated by negatively charged membrane heparan sulfate proteoglycans (HSPGs). α-Synuclein fibrils formed in the presence of copper/iron ions were more cytotoxic, causing increased ROS production, cell apoptosis, and shortened the lifespan of a C. elegans PD model overexpressing human α-synuclein. Notably, these deleterious effects were ameliorated by two clinically used chelators, triethylenetetramine and deferiprone. Together, our results suggest a new role for heavy metal ions, e.g. copper and iron, in the pathogenesis of PD through accelerating prion-like propagation of α-synuclein fibrils.

Application of High-Throughput Competition Experiments in the Development of Aspartate-Directed Site-Selective Modification of Tyrosine Residues in Peptides

Herein we report a Cu-catalyzed, site-selective functionalization of peptides that employs an aspartic acid (Asp) as a native directing motif, which directs the site of O-arylation at a proximal tyrosine (Tyr) residue. Through a series of competition studies conducted in high-throughput reaction arrays, effective conditions were identified that gave high selectivity for the proximal Tyr in Asp-directed Tyr modification. Good levels of site-selectivity were achieved in the O-arylation at a proximal Tyr residue in a number of cases, including a peptide-small molecule hybrid.

Strategies in Translating the Therapeutic Potentials of Host Defense Peptides

The golden era of antibiotics, heralded by the discovery of penicillin, has long been challenged by the emergence of antimicrobial resistance (AMR). Host defense peptides (HDPs), previously known as antimicrobial peptides, are emerging as a group of promising antimicrobial candidates for combatting AMR due to their rapid and unique antimicrobial action. Decades of research have advanced our understanding of the relationship between the physicochemical properties of HDPs and their underlying antimicrobial and non-antimicrobial functions, including immunomodulatory, anti-biofilm, and wound healing properties. However, the mission of translating novel HDP-derived molecules from bench to bedside has yet to be fully accomplished, primarily attributed to their intricate structure-activity relationship, toxicity, instability in host and microbial environment, lack of correlation between in vitro and in vivo efficacies, and dwindling interest from large pharmaceutical companies. Based on our previous experience and the expanding knowledge gleaned from the literature, this review aims to summarize the novel strategies that have been employed to enhance the antimicrobial efficacy, proteolytic stability, and cell selectivity, which are all crucial factors for bench-to-bedside translation of HDP-based treatment. Strategies such as residues substitution with natural and/or unnatural amino acids, hybridization, L-to-D heterochiral isomerization, C- and N-terminal modification, cyclization, incorporation with nanoparticles, and "smart design" using artificial intelligence technology, will be discussed. We also provide an overview of HDP-based treatment that are currently in the development pipeline.

High throughput sequencing of in vitro selections of mRNA-displayed peptides: data analysis and applications

In vitro selection using mRNA display is currently a widely used method to isolate functional peptides with desired properties. The analysis of high throughput sequencing (HTS) data from in vitro evolution experiments has proven to be a powerful technique but only recently has it been applied to mRNA display selections. In this Perspective, we introduce aspects of mRNA display and HTS that may be of interest to physical chemists. We highlight the potential of HTS to analyze in vitro selections of peptides and review recent advances in the application of HTS analysis to mRNA display experiments. We discuss some possible issues involved with HTS analysis and summarize some strategies to alleviate them. Finally, the potential for future impact of advancing HTS analysis on mRNA display experiments is discussed.