Engineered ferritin for lanthanide binding

Fusion of amyloid beta with ferritin yields an isolated oligomeric beta-sheet-rich aggregate inside the ferritin cage

Alzheimer's disease is a severe brain condition caused by the formation of amyloid plaques composed of amyloid beta (Aβ) peptides. These peptides form oligomers, protofibrils, and fibrils before deposition into amyloid plaques. Among these intermediates, Aβ oligomers (AβOs) were found to be the most toxic and therefore an appealing target for drug development and understanding their role in the disease. However, precise isolation and characterization of AβOs have proven challenging because AβOs tend to aggregate and form heterogeneous mixtures in solution. As a solution, we genetically fused the Aβ peptide with a ferritin monomer. Such fusion allowed the encapsulation of precisely 24 Aβ peptides inside the 24-mer ferritin cage. Using high-speed atomic force microscopy (HS-AFM), we disassembled ferritin and directly visualized the Aβ core enclosed within the cage. The thioflavin-T assay (ThT) and attenuated total reflection infrared spectroscopy (ATR-IR) revealed the presence of a β-sheet structure in the encapsulated oligomeric aggregate. Gallic acid, an amyloid inhibitor, can inhibit the fluorescence of ThT bound AβOs. Our approach represents a significant advancement in the isolation and characterization of β-sheet rich AβOs and is expected to be useful for future studies of other disordered peptides such as α-synuclein and tau.

Design of protein-binding peptides with controlled binding affinity: the case of SARS-CoV-2 receptor binding domain and angiotensin-converting enzyme 2 derived peptides

The development of methods able to modulate the binding affinity between proteins and peptides is of paramount biotechnological interest in view of a vast range of applications that imply designed polypeptides capable to impair or favour Protein-Protein Interactions. Here, we applied a peptide design algorithm based on shape complementarity optimization and electrostatic compatibility and provided the first experimental in vitro proof of the efficacy of the design algorithm. Focusing on the interaction between the SARS-CoV-2 Spike Receptor-Binding Domain (RBD) and the human angiotensin-converting enzyme 2 (ACE2) receptor, we extracted a 23-residues long peptide that structurally mimics the major interacting portion of the ACE2 receptor and designed in silico five mutants of such a peptide with a modulated affinity. Remarkably, experimental KD measurements, conducted using biolayer interferometry, matched the in silico predictions. Moreover, we investigated the molecular determinants that govern the variation in binding affinity through molecular dynamics simulation, by identifying the mechanisms driving the different values of binding affinity at a single residue level. Finally, the peptide sequence with the highest affinity, in comparison with the wild type peptide, was expressed as a fusion protein with human H ferritin (HFt) 24-mer. Solution measurements performed on the latter constructs confirmed that peptides still exhibited the expected trend, thereby enhancing their efficacy in RBD binding. Altogether, these results indicate the high potentiality of this general method in developing potent high-affinity vectors for hindering/enhancing protein-protein associations.

Hydrophobicity-enhanced ferritin nanoparticles for efficient encapsulation and targeted delivery of hydrophobic drugs to tumor cells

Ferritin, a naturally occurring iron storage protein, has gained significant attention as a drug delivery platform due to its inherent biocompatibility and capacity to encapsulate therapeutic agents. In this study, we successfully genetically engineered human H ferritin by incorporating 4 or 6 tryptophan residues per subunit, strategically oriented towards the inner cavity of the nanoparticle. This modification aimed to enhance the encapsulation of hydrophobic drugs into the ferritin cage. Comprehensive characterization of the mutants revealed that only the variant carrying four tryptophan substitutions per subunit retained the ability to disassemble and reassemble properly. As a proof of concept, we evaluated the loading capacity of this mutant with ellipticine, a natural hydrophobic indole alkaloid with multimodal anticancer activity. Our data demonstrated that this specific mutant exhibited significantly higher efficiency in loading ellipticine compared to human H ferritin. Furthermore, to evaluate the versatility of this hydrophobicity-enhanced ferritin nanoparticle as a drug carrier, we conducted a comparative study by also encapsulating doxorubicin, a commonly used anticancer drug. Subsequently, we tested both ellipticine and doxorubicin-loaded nanoparticles on a promyelocytic leukemia cell line, demonstrating efficient uptake by these cells and resulting in the expected cytotoxic effect.

Engineered Ferritin with Eu3+ as a Bright Nanovector: A Photoluminescence Study

Ferritin nanoparticles play many important roles in theranostic and bioengineering applications and have been successfully used as nanovectors for the targeted delivery of drugs due to their ability to specifically bind the transferrin receptor (TfR1, or CD71). They can be either genetically or chemically modified for encapsulating therapeutics or probes in their inner cavity. Here, we analyzed a new engineered ferritin nanoparticle, made of the H chain mouse ferritin (HFt) fused with a specific lanthanide binding tag (LBT). The HFt-LBT has one high affinity lanthanide binding site per each of the 24 subunits and a tryptophane residue within the tag that acts as an antenna able to transfer the energy to the lanthanide ions via a LRET process. In this study, among lanthanides, we selected europium for its red emission that allows to reduce overlap with tissue auto-fluorescence. Steady state emission measurements and time-resolved emission spectroscopy have been employed to investigate the interaction between the HFt-LBT and the Eu3+ ions. This allowed us to identify the Eu3+ energy states involved in the process and to pave the way for the future use of HFt-LBT Eu3+ complex in theranostics.

Gastrointestinal Tract Stabilized Protein Delivery Using Disulfide Thermostable Exoshell System

Thermostable exoshells (tES) are engineered proteinaceous nanoparticles used for the rapid encapsulation of therapeutic proteins/enzymes, whereby the nanoplatform protects the payload from proteases and other denaturants. Given the significance of oral delivery as the preferred model for drug administration, we structurally improved the stability of tES through multiple inter-subunit disulfide linkages that were initially absent in the parent molecule. The disulfide-linked tES, as compared to tES, significantly stabilized the activity of encapsulated horseradish peroxidase (HRP) at acidic pH and against the primary human digestive enzymes, pepsin, and trypsin. Furthermore, the disulfide-linked tES (DS-tES) exhibited significant intestinal permeability as evaluated using Caco2 cells. In vivo bioluminescence assay showed that encapsulated Renilla luciferase (rluc) was ~3 times more stable in mice compared to the free enzyme. DS-tES collected mice feces had ~100 times more active enzyme in comparison to the control (free enzyme) after 24 h of oral administration, demonstrating strong intestinal stability. Taken together, the in vitro and in vivo results demonstrate the potential of DS-tES for intraluminal and systemic oral drug delivery applications.

Unlocking the Treasure Box: The Role of HEPES Buffer in Disassembling an Uncommon Ferritin Nanoparticle

Ferritins are ideal nanoparticles as drug delivery systems due to their hollow-sphere structure and the ability to target specific receptors on the cell surface. Here, we develop and characterize a new ferritin derived from the chimeric humanized A. fulgidus one, already designed to recognize the TfR1 receptor. Starting from the synthetic gene of this chimeric protein, we replaced two positively charged amino acids with two alanine residues to close the large triangular pores on its surface. These mutations make the protein nanoparticle suitable to incorporate even small therapeutics without leakage. Size-exclusion chromatography shows that the assembling/disassembling of this new protein cage can be easily fine-tuned by varying the HEPES buffer and MgCl2 concentration. The protein cage can be opened using 150 mM HEPES buffer without magnesium ions. Adding this divalent cation to the solution promotes the quick assembly of the ferritin as a 24-mer. The development of this new protein cage paves the way for encapsulation and delivery studies of small molecules for therapeutic and diagnostic purposes.

Ferritin: A Promising Nanoreactor and Nanocarrier for Bionanotechnology

The essence of bionanotechnology lies in the application of nanotechnology/nanomaterials to solve the biological problems. Quantum dots and nanoparticles hold potential biomedical applications, but their inherent problems such as low solubility and associated toxicity due to their interactions at nonspecific target sites is a major concern. The self-assembled, thermostable, ferritin protein nanocages possessing natural iron scavenging ability have emerged as a potential solution to all the above-mentioned problems by acting as nanoreactor and nanocarrier. Ferritins, the cellular iron repositories, are hollow, spherical, symmetric multimeric protein nanocages, which sequester the excess of free Fe(II) and synthesize iron biominerals (Fe₂O₃·H₂O) inside their ∼5-8 nm central cavity. The electrostatics and dynamics of the pore residues not only drives the natural substrate Fe²⁺ inside ferritin nanocages but also uptakes a set of other metals ions/counterions during in vitro synthesis of nanomaterial. The current review aims to report the recent developments/understanding on ferritin structure (self-assembly, surface/pores electrostatics, metal ion binding sites) and chemistry occurring inside these supramolecular protein cages (protein mediated metal ion uptake and mineralization/nanoparticle formation) along with its surface modification to exploit them for various nanobiotechnological applications. Furthermore, a better understanding of ferritin self-assembly would be highly useful for optimizing the incorporation of nanomaterials via the disassembly/reassembly approach. Several studies have reported the successful engineering of these ferritin protein nanocages in order to utilize them as potential nanoreactor for synthesizing/incorporating nanoparticles and as nanocarrier for delivering imaging agents/drugs at cell specific target sites. Therefore, the combination of nanoscience (nanomaterials) and bioscience (ferritin protein) projects several benefits for various applications ranging from electronics to medicine.

A Review on Drug Delivery System for Tumor Therapy

In recent years, with the development of nanomaterials, the research of drug delivery systems has become a new field of cancer therapy. Compared with conventional antitumor drugs, drug delivery systems such as drug nanoparticles (NPs) are expected to have more advantages in antineoplastic effects, including easy preparation, high efficiency, low toxicity, especially active tumor-targeting ability. Drug delivery systems are usually composed of delivery carriers, antitumor drugs, and even target molecules. At present, there are few comprehensive reports on a summary of drug delivery systems applied for tumor therapy. This review introduces the preparation, characteristics, and applications of several common delivery carriers and expounds the antitumor mechanism of different antitumor drugs in delivery carriers in detail which provides a more theoretical basis for clinical application of personalized cancer nanomedicine in the future.

Spectrophotometric methods to probe the solution chemistry of lanthanide complexes with macromolecules

Lanthanide biochemistry has experienced a revival in recent years owing to the discovery of new biomolecular platforms that are amenable to bind, sequester, or transport lanthanide ions. This has inherently created a need for physicochemical methods that report on lanthanide-containing macromolecular systems. In this chapter, the use of spectrophotometric methods to study the stability of lanthanide-macromolecule complexes in solution is discussed. Indeed, lanthanide ions have unique spectral properties in the ultraviolet, visible, and near-infrared domains that set them apart from the more common elements encountered in biochemistry, and these unique features can be leveraged to study, in a quantitative and robust manner, the solution chemistry of their biorelevant species (K_d, pH stability, temperature profile, etc.). This chapter aims at bringing a method that has been established and validated in the small molecule chemistry field to this new era of lanthanide biochemistry.

A novel strategy for molecular interfaces optimization: The case of Ferritin-Transferrin receptor interaction

Protein-protein interactions regulate almost all cellular functions and rely on a fine tune of surface amino acids properties involved on both molecular partners. The disruption of a molecular association can be caused even by a single residue mutation, often leading to a pathological modification of a biochemical pathway. Therefore the evaluation of the effects of amino acid substitutions on binding, and the ad hoc design of protein-protein interfaces, is one of the biggest challenges in computational biology. Here, we present a novel strategy for computational mutation and optimization of protein-protein interfaces. Modeling the interaction surface properties using the Zernike polynomials, we describe the shape and electrostatics of binding sites with an ordered set of descriptors, making possible the evaluation of complementarity between interacting surfaces. With a Monte Carlo approach, we obtain protein mutants with controlled molecular complementarities. Applying this strategy to the relevant case of the interaction between Ferritin and Transferrin Receptor, we obtain a set of Ferritin mutants with increased or decreased complementarity. The extensive molecular dynamics validation of the method results confirms its efficacy, showing that this strategy represents a very promising approach in designing correct molecular interfaces.

Selective and Efficient Biomacromolecular Extraction of Rare-Earth Elements using Lanmodulin

Lanmodulin (LanM) is a recently discovered protein that undergoes a large conformational change in response to rare-earth elements (REEs). Here, we use multiple physicochemical methods to demonstrate that LanM is the most selective macromolecule for REEs characterized to date and even outperforms many synthetic chelators. Moreover, LanM exhibits metal-binding properties and structural stability unseen in most other metalloproteins. LanM retains REE binding down to pH ≈ 2.5, and LanM-REE complexes withstand high temperature (up to 95 °C), repeated acid treatments, and up to molar amounts of competing non-REE metal ions (including Mg, Ca, Zn, and Cu), allowing the protein's use in harsh chemical processes. LanM's unrivaled properties were applied to metal extraction from two distinct REE-containing industrial feedstocks covering a broad range of REE and non-REE concentrations, namely, precombustion coal and electronic waste leachates. After only a single all-aqueous step, quantitative and selective recovery of the REEs from all non-REEs initially present (Li, Na, Mg, Ca, Sr, Al, Si, Mn, Fe, Co, Ni, Cu, Zn, and U) was achieved, demonstrating the universal selectivity of LanM for REEs against non-REEs and its potential application even for industrial low-grade sources, which are currently underutilized. Our work indicates that biosourced macromolecules such as LanM may offer a new paradigm for extractive metallurgy and other applications involving f-elements.

Rare earth elements (REE) in biology and medicine

This survey reports on topics that were presented at the workshop on “Challenges with Rare Earth Elements. The Periodic Table at work for new Science & Technology” hold at the Academia dei Lincei in November 2019. The herein reported materials refer to presentations dealing with studies and applications of rare earth elements (REE) in several areas of Biology and Medicine. All together they show the tremendous impact REE have in relevant fields of living systems and highlight, on one hand, the still existing knowledge gap for an in-depth understanding of their function in natural systems as well as the very important role they already have in providing innovative scientific and technological solutions in a number of bio-medical areas and in fields related to the assessment of the origin of food and on their manufacturing processes. On the basis of the to-date achievements one expects that new initiatives will bring, in a not too far future, to a dramatic increase of our understanding of the REE involvement in living organisms as well as a ramp-up in the exploitation of the peculiar properties of REE for the design of novel applications in diagnostic procedures and in the set-up of powerful medical devices. This scenario calls the governmental authorities for new responsibilities to guarantee a continuous availability of REE to industry and research labs together with providing support to activities devoted to their recovery/recycling.

Ferritin Nanocages for Protein Delivery to Tumor Cells

The delivery of therapeutic proteins is one of the greatest challenges in the treatment of human diseases. In this frame, ferritins occupy a very special place. Thanks to their hollow spherical structure, they are used as modular nanocages for the delivery of anticancer drugs. More recently, the possibility of encapsulating even small proteins with enzymatic or cytotoxic activity is emerging. Among all ferritins, particular interest is paid to the Archaeoglobus fulgidus one, due to its peculiar ability to associate/dissociate in physiological conditions. This protein has also been engineered to allow recognition of human receptors and used in vitro for the delivery of cytotoxic proteins with extremely promising results.

Ferritin nanovehicle for targeted delivery of cytochrome C to cancer cells

In this work, we have exploited the unique properties of a chimeric archaeal-human ferritin to encapsulate, deliver and release cytochrome c and induce apoptosis in a myeloid leukemia cell line. The chimeric protein combines the versatility in 24-meric assembly and cargo incorporation capability of Archaeglobus fulgidus ferritin with specific binding of human H ferritin to CD71, the "heavy duty" carrier responsible for transferrin-iron uptake. Delivery of ferritin-encapsulated cytochrome C to the Acute Promyelocytic Leukemia (APL) NB4 cell line, highly resistant to transfection by conventional methods, was successfully achieved in vitro. The effective liberation of cytochrome C within the cytosolic environment, demonstrated by double fluorescent labelling, induced apoptosis in the cancer cells.

Application of crossflow ultrafiltration for scaling up the purification of a recombinant ferritin

Ferritin proteins are taking center stage as smart nanocarriers for drug delivery due to their hollow cage-like structures and their unique 24-meric assembly. Among all ferritins, the chimeric Archaeoglobus ferritin (HumFt) is able assemble/disassemble varying the ionic strength of the medium while recognizing human TfR1 receptor overexpressed in cancer cells. In this paper we present a highly efficient, large scale purification protocol mainly based on crossflow ultrafiltration, starting from fermented bacterial paste. This procedure allows one to obtain about 2 g of purified protein starting from 100 g of fermented bacterial paste. The current procedure can easily remove contaminant proteins as well as DNA molecules in the absence of expensive and time consuming chromatographic steps.

Ferritin-based anticancer metallodrug delivery: Crystallographic, analytical and cytotoxicity studies

The encapsulation of anticancer metal-based drugs within a protein nanocage represents a valuable strategy to improve the efficacy and selectivity of these compounds towards cancer cells. The preparation, characterization of the in vitro cytotoxicity and X-ray structures of several ferritin-metallodrug nanocomposites (mainly containing platinum-, ruthenium- and gold-based anticancer agents) are here reviewed. The molecular mechanisms of action of these Ft-metallodrug adducts are discussed and future directions in the field are outlined.

Cryo-EM structure of the human ferritin-transferrin receptor 1 complex

Human transferrin receptor 1 (CD71) guarantees iron supply by endocytosis upon binding of iron-loaded transferrin and ferritin. Arenaviruses and the malaria parasite exploit CD71 for cell invasion and epitopes on CD71 for interaction with transferrin and pathogenic hosts were identified. Here, we provide the molecular basis of the CD71 ectodomain-human ferritin interaction by determining the 3.9 Å resolution single-particle cryo-electron microscopy structure of their complex and by validating our structural findings in a cellular context. The contact surfaces between the heavy-chain ferritin and CD71 largely overlap with arenaviruses and Plasmodium vivax binding regions in the apical part of the receptor ectodomain. Our data account for transferrin-independent binding of ferritin to CD71 and suggest that select pathogens may have adapted to enter cells by mimicking the ferritin access gate.

The human transferrin receptor 1 (CD71) is a transmembrane protein responsible for iron uptake. Here the authors present the 3.9 Å resolution cryo-EM structure of the CD71 ectodomain-human ferritin (H-Ft) complex and find that H-Ft binds a CD71 region different from the transferrin one that overlaps with the surface recognized by select pathogens.