Schlauch D, Güler CS, Harzi M
… +3 more, Kara S, Lavrentieva A, Pepelanova I
Biopolymers
· 2026 May · PMID 41933468
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Hydrogels based on thiol-ene step-growth chemistry have gained increased attention due to their superior properties over the currently standard materials based on chain growth polymerization. In the thiol-ene reaction, a...Hydrogels based on thiol-ene step-growth chemistry have gained increased attention due to their superior properties over the currently standard materials based on chain growth polymerization. In the thiol-ene reaction, a crosslinker with at least two thiol groups is necessary for network formation. Many currently used crosslinkers exhibit cytotoxic potential, are non-biodegradable, or involve toxic chemicals and relatively complicated procedures in their synthesis, thus hindering their broader application. As an alternative, the use of a protein (fibrinogen gamma chain, FGG) recombinantly expressed in Escherichia coli was investigated. The FGG is part of the multimeric fibrinogen involved in hemostasis. This protein complex is stabilized by disulfide crosslinking. This presence of cysteines in the sequence makes FGG a promising candidate as a thiol donor in thiol-ene reactions. It was shown for the first time, that a cysteine-containing protein expressed in E. coli was capable of forming hydrogels with norbornene functionalized gelatin. An increase in FGG concentration led to higher gel stiffness and a decrease in the swelling ratio. Furthermore, the material exhibited cell adhesive properties and biocompatibility. Overall, a proof-of-principle could be achieved, opening up the use of recombinant proteins without further modifications as crosslinkers in thiol-ene based hydrogels, providing a cost-effective, safe, and scalable material source.
Biopolymers
· 2025 May · PMID 40231443
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Antimicrobial peptides (AMPs), produced in various organisms, including plants, as a first line of defense, are potent, functionally versatile, fast-acting small peptides with a net charge and diverse structures. Most AM...Antimicrobial peptides (AMPs), produced in various organisms, including plants, as a first line of defense, are potent, functionally versatile, fast-acting small peptides with a net charge and diverse structures. Most AMPs demonstrate potent antibacterial activity, and AMPs with multimodal actions can potentially delay the development of antimicrobial resistance (AMR), one of the top 10 global public health challenges categorized by the WHO. Notably, the FDA has already approved several AMPs (Mol. Wt. ≤ 2 kDa) as antibiotics; however, there are not enough new-age antibiotics in the current pipeline to combat the looming problem of AMR in the clinic. Nevertheless, despite their potential, natural AMPs have their fair share of shortcomings for straightforward therapeutic applications. Therefore, extensive research on developing designer synthetic AMPs with broad-spectrum antimicrobial activity is currently being undertaken to mitigate the AMR challenge. In this context, we recently demonstrated a short synthetic designer AMP (SR17: ≤ 16 aa, mol. Wt. ≤ 2 kDa) that exhibits broad-spectrum bacteriostatic and bactericidal action against both gram-negative (Escherichia coli, Pseudomonas aeruginosa, Acinetobacter baumannii) and gram-positive (Staphylococcus aureus) bacteria. Interestingly, in gram-negative bacteria, the outer membrane proteins (OMPs) play a key role in transporting nutrients like iron from their surroundings through siderophores, which play a crucial role in various biochemical processes essential for their survival and growth. In the current study, the ability of SR17 to target the iron-transporting OMPs acting as the siderophore uptake system is investigated through computational techniques. A series of docking and molecular dynamics (MD) simulation studies involving iron transporters of various gram-negative bacteria indicate that SR17 can occupy the binding pocket in the OMPs necessary for binding of the iron-chelated siderophores, which is likely to prevent the further uptake of siderophores, affecting the growth and survival of the bacteria. Additionally, SR17 may potentially reach the bacterial cytoplasm by utilizing the siderophore uptake system and disrupt essential cytoplasmic processes, leading to the death of the bacteria, as observed in experimental studies.
Jiang S, Tian Y, Nicolaescu V
… +4 more, Mansurov A, Randall G, Tirrell MV, LaBelle JL
Pept Sci (Hoboken)
· 2024 Nov · PMID 39866902
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The COVID-19 pandemic drove a uniquely fervent pursuit to explore the potential of peptide, antibody, protein, and small-molecule based antiviral agents against severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2...The COVID-19 pandemic drove a uniquely fervent pursuit to explore the potential of peptide, antibody, protein, and small-molecule based antiviral agents against severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2). The interaction between the SARS-CoV2 spike protein with the angiotensin-converting enzyme 2 (ACE2) receptor that mediates viral cell entry was a particularly interesting target given its well described protein-protein interaction (PPI). This PPI is mediated by an α-helical portion of ACE2 binding to the receptor binding domain (RBD) of the spike protein and thought to be susceptible to blockade through molecular mimicry. Small numbers of hydrocarbon-stapled synthetic peptides designed to disrupt or block this interaction were tested individually and were found to have variable efficacy despite having related or overlapping sequences and similarly increased α-helicity. Reasons for these differences are unclear and reported pre-clinical successes have been limited. The current study sought to better understand reasons for these differences through evaluation of a comprehensive collection of hydrocarbon stapled peptides, designed based on four distinct principles: stapling position, number of staples, amino acid sequence, and primary sequence length. Surprisingly, we observed that the helicity and amino acid sequence iterations of hydrocarbon-stapled peptides did not correlate with their bioactivity. Our results highlight the importance of iterative and combinatorial testing of these compounds to determine a configuration that best mimics natural binding and allows for chain flexibility while sacrificing structural helicity.
Selig EE, Bhura R, White MR
… +6 more, Akula S, Hoffman RD, Tovar CN, Xu X, Booth RE, Libich DS
Biopolymers
· 2023 May · PMID 36929870
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EWS is a member of the FET family of RNA/DNA binding proteins that regulate crucial phases of nucleic acid metabolism. EWS comprises an N-terminal low-complexity domain (LCD) and a C-terminal RNA-binding domain (RBD). Th...EWS is a member of the FET family of RNA/DNA binding proteins that regulate crucial phases of nucleic acid metabolism. EWS comprises an N-terminal low-complexity domain (LCD) and a C-terminal RNA-binding domain (RBD). The RBD is further divided into three RG-rich regions, which flank an RNA-recognition motif (RRM) and a zinc finger (ZnF) domain. Recently, EWS was shown to regulate R-loops in Ewing sarcoma, a pediatric bone and soft-tissue cancer in which a chromosomal translocation fuses the N-terminal LCD of EWS to the C-terminal DNA binding domain of the transcription factor FLI1. Though EWS was shown to directly bind R-loops, the binding mechanism was not elucidated. In the current study, the RBD of EWS was divided into several constructs, which were subsequently assayed for binding to various nucleic acid structures expected to form at R-loops, including RNA stem-loops, DNA G-quadruplexes, and RNA:DNA hybrids. EWS interacted with all three nucleic acid structures with varying affinities and multiple domains contributed to binding each substrate. The RRM and RG2 region appear to bind nucleic acids promiscuously while the ZnF displayed more selectivity for single-stranded structures. With these results, the structural underpinnings of EWS recognition and binding of R-loops and other nucleic acid structures is better understood.
Pept Sci (Hoboken)
· 2023 Jan · PMID 36778914
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Peptide vaccines and immunotherapies against aggregating proteins involved in the pathogenesis and progression of Alzheimer's disease (AD) - the β-amyloid peptide (Aβ) and tau - are promising therapeutic avenues against...Peptide vaccines and immunotherapies against aggregating proteins involved in the pathogenesis and progression of Alzheimer's disease (AD) - the β-amyloid peptide (Aβ) and tau - are promising therapeutic avenues against AD. Two decades of effort has led to the controversial FDA approval of the monoclonal antibody Aducanumab (Aduhelm), which has subsequentially sparked the revival and expedited review of promising monoclonal antibody immunotherapies that target Aβ. In this review, we explore the development of Aβ and tau peptide vaccines and immunotherapies with monoclonal antibodies in clinical trials against AD.
Doyle ME, Dalgarno K, Masoero E
… +1 more, Ferreira AM
Biopolymers
· 2023 Jan · PMID 36444710
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With an ageing world population and ~20% of adults in Europe being affected by bone diseases, there is an urgent need to develop advanced regenerative approaches and biomaterials capable to facilitate tissue regeneration...With an ageing world population and ~20% of adults in Europe being affected by bone diseases, there is an urgent need to develop advanced regenerative approaches and biomaterials capable to facilitate tissue regeneration while providing an adequate microenvironment for cells to thrive. As the main components of bone are collagen and apatite mineral, scientists in the tissue engineering field have attempted in combining these materials by using different biomimetic approaches to favour bone repair. Still, an ideal bone analogue capable of mimicking the distinct properties (i.e., mechanical properties, degradation rate, porosity, etc.) of cancellous bone is to be developed. This review seeks to sum up the current understanding of bone tissue mineralisation and structure while providing a critical outlook on the existing biomimetic strategies of mineralising collagen for bone tissue engineering applications, highlighting where gaps in knowledge exist.
Choudhury AR, Maity A, Chakraborty S
… +1 more, Chakrabarti R
Pept Sci (Hoboken)
· 2022 Sep · PMID 35574509
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Since its first detection in 2019, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has been the cause of millions of deaths worldwide. Despite the development and administration of different vaccines, th...Since its first detection in 2019, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has been the cause of millions of deaths worldwide. Despite the development and administration of different vaccines, the situation is still worrisome as the virus is constantly mutating to produce newer variants some of which are highly infectious. This raises an urgent requirement to understand the infection mechanism and thereby design therapeutic-based treatment for COVID-19. The gateway of the virus to the host cell is mediated by the binding of the receptor binding domain (RBD) of the virus spike protein to the angiotensin-converting enzyme 2 (ACE2) of the human cell. Therefore, the RBD of SARS-CoV-2 can be used as a target to design therapeutics. The α1 helix of ACE2, which forms direct contact with the RBD surface, has been used as a template in the current study to design stapled peptide therapeutics. Using computer simulation, the mechanism and thermodynamics of the binding of six stapled peptides with RBD have been estimated. Among these, the one with two lactam stapling agents has shown binding affinity, sufficient to overcome RBD-ACE2 binding. Analyses of the mechanistic detail reveal that a reorganization of amino acids at the RBD-ACE2 interface produces favorable enthalpy of binding whereas conformational restriction of the free peptide reduces the loss in entropy to result higher binding affinity. The understanding of the relation of the nature of the stapling agent with their binding affinity opens up the avenue to explore stapled peptides as therapeutic against SARS-CoV-2.
Biopolymers
· 2021 Oct · PMID 34528703
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Proteins that can reversibly alternate between distinctly different folds under native conditions are described as being metamorphic. The "metamorphome" is the collection of all metamorphic proteins in the proteome, but...Proteins that can reversibly alternate between distinctly different folds under native conditions are described as being metamorphic. The "metamorphome" is the collection of all metamorphic proteins in the proteome, but it remains unknown the extent to which the proteome is populated by this class of proteins. We propose that uncovering the metamorphome will require a synergy of computational screening of protein sequences to identify potential metamorphic behavior and validation through experimental techniques. This perspective discusses computational and experimental approaches that are currently used to predict and characterize metamorphic proteins as well as the need for developing improved methodologies. Since metamorphic proteins act as molecular switches, understanding their properties and behavior could lead to novel applications of these proteins as sensors in biological or environmental contexts.
Bioelectronic devices sense or deliver information at the interface between living systems and electronics by converting biological signals into electronic signals and vice-versa. Biological signals are typically carried...Bioelectronic devices sense or deliver information at the interface between living systems and electronics by converting biological signals into electronic signals and vice-versa. Biological signals are typically carried by ions and small molecules. As such, ion conducting materials are ideal candidates in bioelectronics for an optimal interface. Among these materials, ion conducting polymers that are able to uptake water are particularly interesting because, in addition to ionic conductivity, their mechanical properties can closely match the ones of living tissue. In this review, we focus on a specific subset of ion-conducting polymers: proton (H ) conductors that are naturally derived. We first provide a brief introduction of the proton conduction mechanism, and then outline the chemical structure and properties of representative proton-conducting natural biopolymers: polysaccharides (chitosan and glycosaminoglycans), peptides and proteins, and melanin. We then highlight examples of using these biopolymers in bioelectronic devices. We conclude with current challenges and future prospects for broader use of natural biopolymers as proton conductors in bioelectronics and potential translational applications.
Biopolymers
· 2021 Jan · PMID 33001446
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Chemical modifications on RNA can regulate fundamental biological processes. Recent efforts have illuminated the chemical diversity of posttranscriptional ("epitranscriptomic") modifications on eukaryotic messenger RNA a...Chemical modifications on RNA can regulate fundamental biological processes. Recent efforts have illuminated the chemical diversity of posttranscriptional ("epitranscriptomic") modifications on eukaryotic messenger RNA and have begun to elucidate their biological roles. In this review, we discuss our current molecular understanding of epitranscriptomic RNA modifications and their effects on gene expression. In particular, we highlight the role of modifications in mediating RNA-protein interactions, RNA structure, and RNA-RNA base pairing, and how these macromolecular interactions control biological processes in the cell.
Biopolymers
· 2021 Jan · PMID 32786000
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Bacteria contain a diverse set of RNAs to provide tight regulation of gene expression in response to environmental stimuli. Bacterial small RNAs (sRNAs) work in conjunction with protein cofactors to bind complementary mR...Bacteria contain a diverse set of RNAs to provide tight regulation of gene expression in response to environmental stimuli. Bacterial small RNAs (sRNAs) work in conjunction with protein cofactors to bind complementary mRNA sequences in the cell, leading to up- or downregulation of protein synthesis. In vivo imaging of sRNAs can aid in understanding their spatiotemporal dynamics in real time, which inspires new ways to manipulate these systems for a variety of applications including synthetic biology and therapeutics. Current methods for sRNA imaging are quite limited in vivo and do not provide real-time information about fluctuations in sRNA levels. Herein, we describe our efforts toward the development of an RNA-based fluorescent biosensor for bacterial sRNA both in vitro and in vivo. We validated these sensors for three different bacterial sRNAs in Escherichia coli and demonstrated that the designs provide a bright, sequence-specific signal output in response to exogenous and endogenous RNA targets.
Limitations associated with immunoglobulins have motivated the search for novel binding scaffolds. Repeat proteins have emerged as one promising class of scaffolds, but often are limited to binding protein and peptide ta...Limitations associated with immunoglobulins have motivated the search for novel binding scaffolds. Repeat proteins have emerged as one promising class of scaffolds, but often are limited to binding protein and peptide targets. An exception is the repeat proteins of the immune system, which have in recent years served as an inspiration for binding scaffolds which can bind glycans and other classes of biomolecule. Like other repeat proteins, these proteins can be very stable and have a monomeric mode of binding, with elongated and highly variable binding surfaces. The ability to target glycans and glycoproteins fill an important gap in current tools for research and biomedical applications.
Biopolymers
· 2018 Aug · PMID 29528114
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Cyclic peptides (CPs) are an exciting class of molecules with a variety of applications. However, design strategies for CP therapeutics, for example, are generally limited by a poor understanding of their sequence-struct...Cyclic peptides (CPs) are an exciting class of molecules with a variety of applications. However, design strategies for CP therapeutics, for example, are generally limited by a poor understanding of their sequence-structure relationships. This knowledge gap often leads to a trial-and-error approach for designing CPs for a specific purpose, which is both costly and time-consuming. Herein, we describe the current experimental and computational efforts in understanding and designing head-to-tail CPs along with their respective challenges. In addition, we provide several future directions in the field of computational CP design to improve its accuracy, efficiency and applicability. These advances, combined with experimental techniques, shall ultimately provide a better understanding of these interesting molecules and a reliable working platform to rationally design CPs with desired characteristics.
Chino M, Leone L, Zambrano G
… +8 more, Pirro F, D'Alonzo D, Firpo V, Aref D, Lista L, Maglio O, Nastri F, Lombardi A
Biopolymers
· 2018 Aug · PMID 29468636
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Inspired by natural heme-proteins, scientists have attempted for decades to design efficient and selective metalloporphyrin-based oxidation catalysts. Starting from the pioneering work on small molecule mimics in the lat...Inspired by natural heme-proteins, scientists have attempted for decades to design efficient and selective metalloporphyrin-based oxidation catalysts. Starting from the pioneering work on small molecule mimics in the late 1970s, we have assisted to a tremendous progress in designing cages of different nature and complexity, able to accommodate metalloporphyrins. With the intent of tuning and controlling their reactivity, more and more sophisticated and diverse environments are continuously exploited. In this review, we will survey the current state of art in oxidation catalysis using iron- and manganese-porphyrins housed within designed or engineered protein cages. We will also examine the innovative metal-organic framework (MOF) systems, exploited to achieving an enzyme-like environment around the metalloporphyrin cofactor.
Biopolymers
· 2017 Dec · PMID 29266205
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Chimeric proteins composed of a biologically active peptide and a fragment crystallizable (Fc) domain of immunoglobulin G (IgG) are known as peptibodies. They present an extended half-life due to neonatal Fc receptor (Fc...Chimeric proteins composed of a biologically active peptide and a fragment crystallizable (Fc) domain of immunoglobulin G (IgG) are known as peptibodies. They present an extended half-life due to neonatal Fc receptor (FcRn) salvage pathway, a decreased renal clearance rate owing to its increased size (≈70 kDa) and, depending on the peptide used in the design of the peptibody, an active-targeting moiety. Also, the peptides therapeutic activity is boosted by the number of peptides in the fusion protein (at least two peptides) and to some peptides' alterations. Peptibodies are mainly obtained through recombinant DNA technology. However, to improve peptide properties, "unnatural" changes have been introduced to the original peptides' sequence, for instance, the incorporation of D- or non-natural amino acid residues or even cyclization thus, limiting the application of genetic engineering in the production of peptibodies, since these peptides must be obtained via chemical synthesis. This constrains prompted the development of new methods for conjugation of peptides to Fc domains. Another challenge, subject of intense research, relates to the large-scale production of such peptibodies using these new techniques, which can be minimized by their proved value. To date, two peptibodies, romiplostim and dulaglutide, have been approved and stay as the standard of care in their areas of action. Furthermore, a considerable number of peptibodies are currently in preclinical and clinical development.
Tan ACW, Polo-Cambronell BJ, Provaggi E
… +4 more, Ardila-Suárez C, Ramirez-Caballero GE, Baldovino-Medrano VG, Kalaskar DM
Biopolymers
· 2018 Feb · PMID 29159831
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In the current study, we present the synthesis of novel low cost bio-polyurethane compositions with variable mechanical properties based on castor oil and glycerol for biomedical applications. A detailed investigation of...In the current study, we present the synthesis of novel low cost bio-polyurethane compositions with variable mechanical properties based on castor oil and glycerol for biomedical applications. A detailed investigation of the physicochemical properties of the polymer was carried out by using mechanical testing, ATR-FTIR, and X-ray photoelectron spectroscopy (XPS). Polymers were also tested in short term in-vitro cell culture with human mesenchymal stem cells to evaluate their biocompatibility for potential applications as biomaterial. FTIR analysis confirmed the synthesis of castor oil and glycerol based PU polymers. FTIR also showed that the addition of glycerol as co-polyol increases crosslinking within the polymer backbone hence enhancing the bulk mechanical properties of the polymer. XPS data showed that glycerol incorporation leads to an enrichment of oxidized organic species on the surface of the polymers. Preliminary investigation into in vitro biocompatibility showed that serum protein adsorption can be controlled by varying the glycerol content with polymer backbone. An alamar blue assay looking at the metabolic activity of the cells indicated that castor oil based PU and its variants containing glycerol are non-toxic to the cells. This study opens an avenue for using low cost bio-polyurethane based on castor oil and glycerol for biomedical applications.
Dirksen A, Davis KA, Collins JT
… +10 more, Bhattacharya K, Finneman JI, Pepin EL, Ryczek JS, Brown PW, Wellborn WB, Mangalathillam R, Evans BP, Pozzo MJ, Finn RF
A scalable, viable process was developed for the Fibroblast Growth Factor 21 (FGF21) protein-antibody conjugate, CVX-343, an extended half-life therapeutic for the treatment of metabolic disease. CVX-343 utilizes the Cov...A scalable, viable process was developed for the Fibroblast Growth Factor 21 (FGF21) protein-antibody conjugate, CVX-343, an extended half-life therapeutic for the treatment of metabolic disease. CVX-343 utilizes the CovX antibody scaffold technology platform that was specifically developed for peptide and protein half-life extension. CVX-343 is representative of a growing number of complex novel peptide- and protein-based bioconjugate molecules currently being explored as therapeutic candidates. The complexity of these bioconjugates, assembled using well-established chemistries, can lead to very difficult production schemes requiring multiple starting materials and a combination of diverse technologies. Key improvements had to be made to the original CVX-343 Phase 1 manufacturing process in preparation for Phase 3 and commercial manufacturing. A strategy of minimizing FGF21 dimerization and stabilizing the FGF21 Drug Substance Intermediate (DSI), linker, and activated FGF21 intermediate was pursued. The use of tris(2-carboxyethyl)phosphine (TCEP) to prevent FGF21 dimerization through disulfide formation was eliminated. FGF21 dimerization and linker hydrolysis were minimized by formulating and activating FGF21 at acidic instead of neutral pH. An activation use test was utilized to guide FGF21 pooling in order to minimize misfolds, dimers, and misfolded dimers in the FGF21 DSI. After final optimization of reaction conditions, a process was established that reduced the consumption of FGF21 by 36% (from 4.7 to 3.0 equivalents) and the consumption of linker by 55% (from 1.4 to 0.95 equivalents for a smaller required amount of FGF21 ). The overall process time was reduced from ∼5 to ∼3 days. The product distribution improved from containing ∼60% to ∼75% desired bifunctionalized (+2 FGF21) FGF21-antibody conjugate in the crude conjugation mixture and from ∼80% to ∼85% in the final CVX-343 Drug Substance (DS), while maintaining the same overall process yield based on antibody scaffold input.
Although thionamides would have been first prepared two centuries ago and their chemical and spectroscopic properties extensively investigated, only much more recently (since about 1985) a well deserved but still insuffi...Although thionamides would have been first prepared two centuries ago and their chemical and spectroscopic properties extensively investigated, only much more recently (since about 1985) a well deserved but still insufficient attention has been paid to their endothioxopeptide subfamily which nonetheless currently represents a rapidly emerging area of great scientific interest in the broader field of foldameric compounds based on biologically relevant building blocks. After two brief sections offering information on the unfortunately still limited number of endothioxopeptides discovered from natural sources but also on the impressive advancements registered in the last few years in their synthetic methods, this review article outlines the results of a detailed literature survey on the ongoing great, but not systematic, progress related to the conformational consequences generated by incorporating one (or more) thionamide group(s) into a polypeptide chain. Finally, a short discussion of the growing, but still in its infancy, class of the endoselenoxopeptide congeners is also presented.
Biopolymers
· 2016 Nov · PMID 27352774
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Monoclonal antibodies can bind with high affinity and high selectivity to their targets. As a tool in therapeutics or diagnostics, however, their large size (∼150 kDa) reduces penetration into tissue and prevents passive...Monoclonal antibodies can bind with high affinity and high selectivity to their targets. As a tool in therapeutics or diagnostics, however, their large size (∼150 kDa) reduces penetration into tissue and prevents passive cellular uptake. To overcome these and other problems, minimized protein scaffolds have been chosen or engineered, with care taken to not compromise binding affinity or specificity. An alternate approach is to begin with a minimal non-antibody scaffold and select functional ligands from a de novo library. We will discuss the structure, production, applications, strengths, and weaknesses of several classes of antibody-derived ligands, that is, antibodies, intrabodies, and nanobodies, and nonantibody-derived ligands, that is, monobodies, affibodies, and macrocyclic peptides. In particular, this review is focussed on macrocyclic peptides produced by the Random non-standard Peptides Integrated Discovery (RaPID) system that are small in size (typically ∼2 kDa), but are able to perform tasks typically handled by larger proteinaceous ligands.