Macrocyclic peptides as regulators of protein-protein interactions

Protein-protein interactions are attractive but challenging targets for drug discovery. Recent technological progress and examples using macrocyclic peptides as protein interaction modulators are reviewed.     

Current development of bicyclic peptides

Bicyclic peptides, a class of polypeptides with two loops within their structure, have emerged as powerful tools in the development of new peptide drugs. They have the potential to bind to challenged drug targets, with antibody-like affinity and selectivity. Meanwhile, bicyclic peptides possess small molecule-like access to chemical synthesis, which is conducive to large-scale synthesis and screening. In the last five years, bicyclic peptide technology has been increasingly developed, and researchers have carried out a variety of studies to elucidate the potential functions of bicyclic peptides. With the continuous development of synthetic methods and the advances of new technology to build bicyclic peptide libraries, bicyclic peptides are now becoming widely used in the development of new drugs for various diseases. This perspective provides an overview of the structure types, synthesis and applications of bicyclic peptides in current drug development, and our own views on future challenges of bicyclic peptides.     

Von der molekularen Erkennung zum Design neuer Wirkstoffe: Peptiden auf den Leib geschneidert

The molecular recognition of peptides or peptide fragments by synthetic receptor molecules is of great importance for the design of biosensors, the targeting of cellular processes and hence the development of new therapeutics. Unfortunately, our general understanding of non‐covalent interactions is no yet elaborated enough to create a tailor made receptor starting from zero. One possible approach is therefore to mimic the principles and binding motifs found in nature and further evolve them in to effective receptor molecules using either rational structure variations or a more random combinatorial synthesis. The usefullness and prospective potential of these approaches is illustrated with two case studies showing how one tries to find new strategies to fight bacterial infections and cancer with the help of artificial peptide receptors.     

Self-assembling peptide scaffolds for regenerative medicine

Biomaterials made from self-assembling, short peptides and peptide derivatives have great potential to generate powerful new therapies in regenerative medicine. The high signaling capacity and therapeutic efficacy of peptidic scaffolds has been established in several animal models, and the development of more complex, hierarchical structures based on peptide materials is underway. This highlight discusses several classes of self-assembling peptide-based materials, including peptide amphiphiles, Fmoc-peptides, self-complementary ionic peptides, hairpin peptides, and others. The self-assembly designs, bioactive signalling strategies, and cell signalling capabilities of these bioactive materials are reported. The future challenges of the field are also discussed, including short-term goals such as integration with biopolymers and traditional implants, and long term goals, such as immune system programming, subcellular targeting, and the development of highly integrated scaffold systems.     

1,2,3-Triazoles as Biomimetics in Peptide Science

Natural peptides are an important class of chemical mediators, essential for most vital processes. What limits the potential of the use of peptides as drugs is their low bioavailability and enzymatic degradation in vivo. To overcome this limitation, the development of new molecules mimicking peptides is of great importance for the development of new biologically active molecules. Therefore, replacing the amide bond in a peptide with a heterocyclic bioisostere, such as the 1,2,3-triazole ring, can be considered an effective solution for the synthesis of biologically relevant peptidomimetics. These 1,2,3-triazoles may have an interesting biological activity, because they behave as rigid link units, which can mimic the electronic properties of amide bonds and show bioisosteric effects. Additionally, triazole can be used as a linker moiety to link peptides to other functional groups.     

Phage display of combinatorial peptide libraries: application to antiviral research

Given the growing number of diseases caused by emerging or endemic viruses, original strategies are urgently required: (1) for the identification of new drugs active against new viruses and (2) to deal with viral mutants in which resistance to existing antiviral molecules has been selected. In this context, antiviral peptides constitute a promising area for disease prevention and treatment. The identification and development of these inhibitory peptides require the high-throughput screening of combinatorial libraries. Phage-display is a powerful technique for selecting unique molecules with selective affinity for a specific target from highly diverse combinatorial libraries. In the last 15 years, the use of this technique for antiviral purposes and for the isolation of candidate inhibitory peptides in drug discovery has been explored. We present here a review of the use of phage display in antiviral research and drug discovery, with a discussion of optimized strategies combining the strong screening potential of this technique with complementary rational approaches for identification of the best target. By combining such approaches, it should be possible to maximize the selection of molecules with strong antiviral potential.     

Cell-specific delivery of a chemotherapeutic to lung cancer cells

We report that lung cancer-targeting peptides isolated from a peptide library can be used to deliver an active chemotherapeutic in a cell-specific fashion. The peptides were removed from the context of the phage and placed on a pegylated tetrameric scaffold. The tetrameric peptides were shown to block uptake of their cognate phage. The tetrameric peptides were coupled to doxorubicin, and their cytotoxicity against a panel of different cell lines was tested. Our data demonstrate that these targeting peptides can deliver an active anticancer agent in a cell-specific fashion, resulting in an increase of the therapeutic index of the targeted drug compared to systemic delivery. The efficacy of the peptide conjugate correlates to the affinity of the targeting peptide for a particular cell line. As such, we have demonstrated that cell-specific targeted drugs can be synthesized, even when the cell surface target is unknown.     

Natural Compounds against Alzheimer’s Disease: Molecular Recognition of Aβ1–42 Peptide by Salvia sclareoides Extract and its Major Component,Rosmarinic Acid,as Investigated by NMR

Amyloid peptides, Aβ1–40 and Aβ1–42, represent major molecular targets to develop potential drugs and diagnostic tools for Alzheimer’s Disease (AD). In fact, oligomeric and fibrillar aggregates generated by these peptides are amongst the principal components of amyloid plaques found post mortem in patients suffering from AD. Rosmarinic acid has been demonstrated to be effective in preventing the aggregation of amyloid peptides in vitro and to delay the progression of the disease in animal models. Nevertheless, no information is available about its molecular mechanism of action. Herein, we report the NMR characterization of the interaction of Salvia sclareoides extract and that of its major component, rosmarinic acid, with Aβ1–42 peptide, whose oligomers have been described as the most toxic Aβ species in vivo. Our data shed light on the structural determinants of rosmarinic acid–Aβ1–42 oligomers interaction, thus allowing the elucidation of its mechanism of action. They also provide important information for the rational design of new compounds with higher affinity for Aβ peptides to generate new anti‐amyloidogenic molecules and/or molecular tools for the specific targeting of amyloid aggregates in vivo. In addition, we identified methyl caffeate, another natural compound present in different plants and human diet, as a good ligand of Aβ1–42 oligomers, which also shows anti‐amyloidogenic activity. Finally, we demonstrated the possibility to exploit STD‐NMR and trNOESY experiments to screen extracts from natural sources for the presence of Aβ peptide ligands.     

Peptide-Based Nanomaterials for Tumor Immunotherapy

With the increasing understanding of tumor immune circulation mechanisms, tumor immunotherapy including immune checkpoint blockade has become a research hotspot, which requires the development of more accurate and more efficient drugs with fewer side effects. In line with this requirement, peptides with good biocompatibility, targeting, and specificity become favorable theranostic reagents, and a series of promising candidates for tumor immunotherapy based on peptides have been developed. Additionally, the advantages of nanomaterials as drug carriers such as higher affinity have been demonstrated, providing possibilities of combination therapy. In this review, we summarize the development of peptide-based nanomaterials in tumor immunotherapy from the two aspects of functionalization and self-assembly. Furthermore, new methods for peptide screening, especially machine-learning-related strategies, is also a topic we were interested in, as this forms the basis for the construction of peptide-based platforms. Peptides provide broad prospects for tumor immunotherapy and we hope that this summary can provide insight into possible avenues for future exploration.     

Polymeric particulates to improve oral bioavailability of peptide drugs

Oral administration remains the most convenient way of delivering drugs. Recent advances in biotechnology have produced highly potent new molecules such as peptides, proteins and nucleic acids. Due to their sensitivity to chemical and enzymatic hydrolysis as well as a poor cellular uptake, their oral bioavailability remains very low. Despite sophisticated new delivery systems, the development of a satisfactory oral formulation remains a challenge. Among the possible strategies to improve the absorption of drugs, micro- and nanoparticles represent an exciting approach to enhance the uptake and transport of orally administered molecules. Increasing attention has been paid to their potential use as carriers for peptide drugs for oral administration. This article reviews the most common manufacturing methods for polymeric particles and the physiology of particle absorption from the gastrointestinal (GI) tract. In a second part, the use of polymeric particulate systems to improve the oral absorption of insulin is discussed.     

Construction of peptide-vehicles,bioconjugates having modules for cancer cell surface capture and cell-penetrating peptide with anticancer agents

Recently molecular targeting therapy has been applied to cancer chemotherapy, although in some cases side-effects are not negligible. Based on our bio-detection concept, that is, protein–protein interaction can be mimicked by using peptides, a novel cell-targeting concept designated peptide-vehicle has been proposed, which has conjugates consisting of the cancer cell recognition and cell penetrating peptides with anticancer drugs. The cancer cell surface protein can be captured by a cyclotide, containing protease resistant d-cystine. A library of cell penetrating peptides has been prepared and conjugated to the cyclotide. Anticancer molecules were recovered after clinical use, which were pooled, purified, and derivatized for loading into the vehicle. The present Letter describes construction of peptide-vehicles, bioconjugates focusing on more efficiency and cancer cell selective delivery for anticancer drugs.     

Design of synthetic peptidic constructs for the vaccine development against viral infections

The practical development of modern vaccines has been greatly advanced by the availability of synthetic antigens. The use of such synthetic antigens might be more acceptable for human therapy since synthetic peptides do not have any of the potential dangers associated with the induction of an infection by recombinant viruses. However, synthetic peptides alone are often not immunogenic enough, and a strong immunoadjuvant is usually employed for their elaboration. Unfortunately, only a few adjuvants used in experimental models are allowed for use in human beings. In this regard, different presentations of synthetic peptides such as incorporation into liposomes, modification of the lipophilic properties by means of a covalently coupled fatty acid moiety and the synthesis of larger constructs such as multiple antigenic peptides (MAP) have been demonstrated to yield efficient immunological reagents for the amplification in the analysis and induction of immune responses to a variety of infectious agents. This review outlines recent research on synthetic peptide immunology. The development of a MAP with a built-in adjuvant is highlighted as a robust method for vaccine design.     

An Integrated Proteomics and Bioinformatics Analysis of the Anticancer Properties of RT2 Antimicrobial Peptide on Human Colon Cancer (Caco-2) Cells

New selective, efficacious chemotherapy agents are in demand as traditional drugs display side effects and face growing resistance upon continued administration. To this end, bioactive molecules such as peptides are attracting interest. RT2 is a cationic peptide that was used as an antimicrobial but is being repurposed for targeting cancer. In this work, we investigate the mechanism by which this peptide targets Caco-2 human colon cancer cells, one of the most prevalent and metastatic cancers. Combining label-free proteomics with bioinformatics data, our data explore over 1000 proteins to identify 133 proteins that are downregulated and 79 proteins that are upregulated upon treatment with RT2. These changes occur in a dose-dependent manner and suggest the former group are related to anticancer cell proliferation; the latter group is closely related to apoptosis levels. The mRNA levels of several genes (FGF8, PAPSS2, CDK12, LDHA, PRKCSH, CSE1L, STARD13, TLE3, and OGDHL) were quantified using RT-qPCR and were found to be in agreement with proteomic results. Collectively, the global change in Caco-2 cell protein abundance suggests that RT2 triggers multiple mechanisms, including cell proliferation reduction, apoptosis activation, and alteration of cancerous cell metabolism.     

Snake Venom Components: Tools and Cures to Target Cardiovascular Diseases

Cardiovascular diseases (CVDs) are considered as a major cause of death worldwide. Therefore, identifying and developing therapeutic strategies to treat and reduce the prevalence of CVDs is a major medical challenge. Several drugs used for the treatment of CVDs, such as captopril, emerged from natural products, namely snake venoms. These venoms are complex mixtures of bioactive molecules, which, among other physiological networks, target the cardiovascular system, leading to them being considered in the development and design of new drugs. In this review, we describe some snake venom molecules targeting the cardiovascular system such as phospholipase A2 (PLA2), natriuretic peptides (NPs), bradykinin-potentiating peptides (BPPs), cysteine-rich secretory proteins (CRISPs), disintegrins, fibrinolytic enzymes, and three-finger toxins (3FTXs). In addition, their molecular targets, and mechanisms of action—vasorelaxation, inhibition of platelet aggregation, cardioprotective activities—are discussed. The dissection of their biological effects at the molecular scale give insights for the development of future snake venom-derived drugs.     

Sugar amino acid based scaffolds--novel peptidomimetics and their potential in combinatorial synthesis

To meet the growing demands for the development of new molecular entities for discovering new drugs and materials, organic chemists have started looking for new concepts to supplement traditional approaches. In one such approach, the expertise gained over the years in the area of organic synthesis and the rational drug-design concepts are combined together to create "nature-like" and yet unnatural organic molecules that are expected to provide leads in discovering new molecules. Emulating the basic principles followed by nature to build its vast repertoire of biomolecules, organic chemists are developing many novel multifunctional building blocks. Sugar amino acids constitute an important class of such polyfunctional scaffolds where the carboxyl, amino and hydroxyl groups provide an excellent opportunity for organic chemists to create structural diversities akin to nature's molecular arsenal. Recent advances in the area of combinatorial chemistry give unprecedented technological support for rapid compilations of sugar amino acid-based libraries exploiting the diversities of carbohydrate molecules and well-developed solid-phase peptide synthesis methods. This review chronicles the development of sugar amino acids as a novel class of peptidomimetic building blocks and their applications in generating desired secondary structures in peptides as well as in creating mimics of natural biopolymers.     

An efficient method for the solid-phase synthesis of fluorescently labelled peptides

Fluorescent labelling of peptides is necessary in a wide range of cell biological applications. In the last decade, the application of cell-penetrating molecules has been advanced by the use of peptides, which have proven efficient in aiding nonpermeant molecules to cross the cell membrane. Currently, the development of new cell-penetrating peptides based on the design and synthesis of labelled peptide libraries is becoming critically important. Here we report an improved method for the solid-phase labelling of peptides, mediated by the activation of 5(6)-carboxyfluorescein with PyAOP/ HOAt.     

Deduction of structural information of interfacial proteins by combined vibrational spectroscopic methods

We demonstrate both theoretically and experimentally that the combination of vibrational spectroscopic techniques on samples can be used to deduce more detailed structural information of interfacial proteins and peptides. Such an approach can be used to elucidate structures of proteins or peptides at interfaces, such as at the solid/liquid interface or in cell membranes. We also discuss that the controlled perturbations may provide more measured parameters for structural studies on such proteins and peptides. In this paper, we will demonstrate that optical spectroscopic techniques such as polarized Fourier transform infrared spectroscopy (FTIR), sum frequency generation (SFG) vibrational spectroscopy, and higher order nonlinear vibrational spectroscopies can be used to deduce different and complementary structural information of molecules at interfaces (e.g., orientation information of certain functional groups and secondary structures of interfacial proteins). Also, we believe that controlled perturbations on samples, such as variation of sample temperature, application of electrical fields, and alternation of substrate roughness, can provide more detailed information regarding the interfacial structures of proteins and peptides. The development of nonlinear vibrational spectroscopies, such as SFG and four-wave mixing vibrational spectroscopy, to examine interfacial protein and peptide structures, and introduction of external perturbations on samples should be able to substantially advance our knowledge in understanding structures and thus functions of proteins and peptides at interfaces.     

Advances in the Development of SARS-CoV-2 Mpro Inhibitors

Since the outbreak of COVID-19, one of the strategies used to search for new drugs has been to find inhibitors of the main protease (Mpro) of the virus SARS-CoV-2. Initially, previously reported inhibitors of related proteases such as the main proteases of SARS-CoV and MERS-CoV were tested. A huge effort was then carried out by the scientific community to design, synthesize and test new small molecules acting as inactivators of SARS-CoV-2 Mpro. From the chemical structure view, these compounds can be classified into two main groups: one corresponds to modified peptides displaying an adequate sequence for high affinity and a reactive warhead; and the second is a diverse group including chemical compounds that do not have a peptide framework. Although a drug including a SARS-CoV-2 main protease inhibitor has already been commercialized, denoting the importance of this field, more compounds have been demonstrated to be promising potent inhibitors as potential antiviral drugs.     

Streamlined in vivo selection and screening of human prostate carcinoma avid phage particles for development of peptide based in vivo tumor imaging agents

Bacteriophage (phage) display has been exploited for the purpose of discovering new cancer specific targeting peptides. However, this approach has resulted in only a small number of tumor targeting peptides useful as in vivo imaging agents. We hypothesize that in vivo screening for tumor uptake of fluorescently tagged phage particles displaying multiple copies of an in vivo selected tumor targeting peptide will expedite the development of peptide based imaging agents. In this study, both in vivo selection and in vivo screening of phage displaying foreign peptides were utilized to best predict peptides with the pharmacokinetic properties necessary for translation into efficacious in vivo imaging agents. An in vivo selection of phage display libraries was performed in SCID mice bearing human PC-3 prostate carcinoma tumors. Eight randomly selected phage clones and four control phage clones were fluorescently labeled with AlexaFluor 680 for subsequent in vivo screening and analyses. The corresponding peptides of six of these phage clones were tested as 111In-labeled peptide conjugates for single photon emission computed tomography (SPECT) imaging of PC-3 prostate carcinomas. Two peptide sequences, G1 and H5, were successful as in vivo imaging agents. The affinities of G1 and H5 peptides for cultured PC-3 cells were then analyzed via cell flow cytometry resulting in Kd values of 1.8 μM and 2.2 μM, respectively. The peptides bound preferentially to prostate tumor cell lines compared to that of other carcinoma and normal cell lines, and H5 appeared to possess cytotoxic properties. This study demonstrates the value of in vivo screening of fluorescently labeled phage for the prediction of the efficacy of the corresponding 111In-labeled synthetic peptide as an in vivo SPECT tumor imaging agent.