Combining Solid-State NMR with Structural and Biophysical Techniques to Design Challenging Protein-Drug Conjugates

Several protein-drug conjugates are currently being used in cancer therapy. These conjugates rely on cytotoxic organic compounds that are covalently attached to the carrier proteins or that interact with them via non-covalent interactions. Human transthyretin (TTR), a physiological protein, has already been identified as a possible carrier protein for the delivery of cytotoxic drugs. Here we show the structure-guided development of a new stable cytotoxic molecule based on a known strong binder of TTR and a well-established anticancer drug. This example is used to demonstrate the importance of the integration of multiple biophysical and structural techniques, encompassing microscale thermophoresis, X-ray crystallography and NMR. In particular, we show that solid-state NMR has the ability to reveal effects caused by ligand binding which are more easily relatable to structural and dynamical alterations that impact the stability of macromolecular complexes.

Solid-state NMR - a complementary technique for protein framework characterization

Protein frameworks are an emerging class of biomaterial with medical and technological applications. Frameworks are studied mainly by X-ray diffraction or scattering techniques. Complementary strategies are required. Here, we report solid-state NMR analyses of a microcrystalline protein-macrocycle framework and the rehydrated freeze-dried protein. This methodology may aid the characterization of low-crystallinity frameworks.

Solid-state NMR methods for the characterization of bioconjugations and protein-material interactions

Protein solid-state NMR has evolved dramatically over the last two decades, with the development of new hardware and sample preparation methodologies. This technique is now ripe for complex applications, among which one can count bioconjugation, protein chemistry and functional biomaterials. In this review, we provide our account on this aspect of protein solid-state NMR.

Epitope Mapping and Binding Assessment by Solid-State NMR Provide a Way for the Development of Biologics under the Quality by Design Paradigm

Multispecific biologics are an emerging class of drugs, in which antibodies and/or proteins designed to bind pharmacological targets are covalently linked or expressed as fusion proteins to increase both therapeutic efficacy and safety. Epitope mapping on the target proteins provides key information to improve the affinity and also to monitor the manufacturing process and drug stability. Solid-state NMR has been here used to identify the pattern of the residues of the programmed cell death ligand 1 (PD-L1) ectodomain that are involved in the interaction with a new multispecific biological drug. This is possible because the large size and the intrinsic flexibility of the complexes are not limiting factors for solid-state NMR.

1H-Detected Biomolecular NMR under Fast Magic-Angle Spinning

Since the first pioneering studies on small deuterated peptides dating more than 20 years ago, 1H detection has evolved into the most efficient approach for investigation of biomolecular structure, dynamics, and interactions by solid-state NMR. The development of faster and faster magic-angle spinning (MAS) rates (up to 150 kHz today) at ultrahigh magnetic fields has triggered a real revolution in the field. This new spinning regime reduces the 1H-1H dipolar couplings, so that a direct detection of 1H signals, for long impossible without proton dilution, has become possible at high resolution. The switch from the traditional MAS NMR approaches with 13C and 15N detection to 1H boosts the signal by more than an order of magnitude, accelerating the site-specific analysis and opening the way to more complex immobilized biological systems of higher molecular weight and available in limited amounts. This paper reviews the concepts underlying this recent leap forward in sensitivity and resolution, presents a detailed description of the experimental aspects of acquisition of multidimensional correlation spectra with fast MAS, and summarizes the most successful strategies for the assignment of the resonances and for the elucidation of protein structure and conformational dynamics. It finally outlines the many examples where 1H-detected MAS NMR has contributed to the detailed characterization of a variety of crystalline and noncrystalline biomolecular targets involved in biological processes ranging from catalysis through drug binding, viral infectivity, amyloid fibril formation, to transport across lipid membranes.

Evaluation of the Higher Order Structure of Biotherapeutics Embedded in Hydrogels for Bioprinting and Drug Release

Biocompatible hydrogels for tissue regeneration/replacement and drug release with specific architectures can be obtained by three-dimensional bioprinting techniques. The preservation of the higher order structure of the proteins embedded in the hydrogels as drugs or modulators is critical for their biological activity. Solution nuclear magnetic resonance (NMR) experiments are currently used to investigate the higher order structure of biotherapeutics in comparability, similarity, and stability studies. However, the size of pores in the gel, protein-matrix interactions, and the size of the embedded proteins often prevent the use of this methodology. The recent advancements of solid-state NMR allow for the comparison of the higher order structure of the matrix-embedded and free isotopically enriched proteins, allowing for the evaluation of the functionality of the material in several steps of hydrogel development. Moreover, the structural information at atomic detail on the matrix-protein interactions paves the way for a structure-based design of these biomaterials.

Structure and Dynamics Perturbations in Ubiquitin Adsorbed or Entrapped in Silica Materials Are Related to Disparate Surface Chemistries Resolved by Solid-State NMR Spectroscopy

Protein immobilization on material surfaces is emerging as a powerful tool in the design of devices and active materials for biomedical and pharmaceutical applications as well as for catalysis. Preservation of the protein's biological functionality is crucial to the design process and is dependent on the ability to maintain its structural and dynamical integrity while removed from the natural surroundings. The scientific techniques to validate the structure of immobilized proteins are scarce and usually provide limited information as a result of poor resolution. In this work, we benchmarked the ability of standard solid-state NMR techniques to resolve the effects of binding to dissimilar silica materials on a model protein. In particular, the interactions between ubiquitin and the surfaces of MCM41, SBA15, and silica formed in situ were tested for their influence on the structure and dynamics of the protein. It is shown that the protein's globular fold in the free state is only slightly perturbed in the three silica materials. Local motions on a residue level that are quenched by immobilization or, conversely, that arise from the process are also detailed. NMR measurements show that these perturbations are unique to each silica material and can serve as reporters of the characteristic surface chemistry.

On the Mechanism of Bioinspired Formation of Inorganic Oxides: Structural Evidence of the Electrostatic Nature of the Interaction between a Mononuclear Inorganic Precursor and Lysozyme

Nature has evolved several molecular machineries to promote the formation at physiological conditions of inorganic materials, which would otherwise be formed in extreme conditions. The molecular determinants of this process have been established over the last decade, identifying a strong role of electrostatics in the first steps of the precipitation. However, no conclusive, structure-based evidence has been provided so far. In this manuscript, we test the binding of lysozyme with silica and titania potential precursors. In contrast with the absence of structural information about the interaction with the silica precursor, we observe the interaction with a mononuclear titanium(IV) species, which is found to occur in a region rich of positive charges.

NMR of Immobilized Enzymes

Solid-state NMR has become the method of choice for the assessment of protein structure for insoluble objects lacking long-range order. In this context, it is apparent that solid-state NMR is also perfectly poised toward the characterization of immobilized proteins. For these systems, it is possible to understand at the atomic level which perturbations, if any, are occurring as a result of the functionalization. Here we describe how it is possible to accomplish the NMR characterization of enzymes that have been immobilized through different approaches, and we introduce the reader to the choice of the experimental strategy that can be useful in different cases. An outlook on the level of information that can be attained is also given, in view of recent methodological advancements.

On the relationship between structure and catalytic effectiveness in solid surface-immobilized enzymes: Advances in methodology and the quest for a single-molecule perspective

The integration of enzymes with solid materials is important in many biotechnological applications, including the use of immobilized enzymes for biocatalytic synthesis. The development of functional enzyme-material composites is restrained by the lack of molecular-level insight into the behavior of enzymes in confined, surface-near environments. Here, we review recent advances in surface-sensitive spectroscopic techniques that push boundaries for the determination of enzyme structure and orientation at the solid-liquid interface. We discuss recent evidence from single-molecule studies showing that analyses sensitive to the temporal and spatial heterogeneities in immobilized enzymes can succeed in disentangling the effects of conformational stability and active-site accessibility on activity. Different immobilization methods involve distinct trade-off between these effects, thus emphasizing the need for a holistic (systems) view of immobilized enzymes for the rational development of practical biocatalysts.

Mechanism and Inhibition of Matrix Metalloproteinases

Matrix metalloproteinases hydrolyze proteins and glycoproteins forming the extracellular matrix, cytokines and growth factors released in the extracellular space, and membrane-bound receptors on the outer cell membrane. The pathological relevance of MMPs has prompted the structural and functional characterization of these enzymes and the development of synthetic inhibitors as possible drug candidates. Recent studies have provided a better understanding of the substrate preference of the different members of the family, and structural data on the mechanism by which these enzymes hydrolyze the substrates. Here, we report the recent advancements in the understanding of the mechanism of collagenolysis and elastolysis, and we discuss the perspectives of new therapeutic strategies for targeting MMPs.

Nanoparticles for the multivalent presentation of a TnThr mimetic and as tool for solid state NMR coating investigation

The fully characterization of tumor associated antigens (TAAs) and of tumor associated carbohydrate antigens (TACAs) have opened the avenue of cancer immunotherapy. The intrinsic poor immunogenicity of TACAs, however, spotlighted the importance of multivalent presentation of the antigen(s) to trigger an immune response. Nanoparticles are excellent scaffolds for this purpose. Here we reported on the easy glycosylation of iron-based and biocompatible dextran-based nanoparticles with 1, a mimetic of the TnThr antigen. The multivalent presentation of 1 induced the induction of TNF-α and IL-6/IL10, respectively. The multivalent glycosylation of silica nanoparticles (GSiNPs) was also performed and saccharide loading qualitative assessed by solid state NMR. Our results offer the proof of concept that biomolecules coating can also be investigated on solid system by NMR.

Atom Probe Tomography for 3D Structural and Chemical Analysis of Individual Proteins

Determination of the 3D structure of proteins and other biomolecules is a major goal in structural biology, to provide insights to their biological function. Such structures are historically unveiled experimentally by X-ray crystallography or NMR spectroscopy, and in recent years using cryo-electron microscopy. Here, a method for structural analysis of individual proteins on the sub-nanometer scale using atom probe tomography is described. This technique offers a combination of high-resolution analysis of biomolecules in 3D, and the chemical sensitivity of mass spectrometry. As a model protein, the well-characterized antibody IgG is used. IgG is encapsulated in an amorphous solid silica matrix via a sol-gel process to provide the requisite support for atom probe analysis. The silica synthesis is tuned to resemble physiological conditions. The 3D reconstructions show good agreement with the protein databank IgG crystal structure. This suggests that the silica-embedding strategy can open the field of atom probe tomography to the analysis of biological molecules. In addition to high-resolution structural information, the technique may potentially provide chemical information on the atomic scale using isotopic labeling. It is envisaged that this method may constitute a useful complement to existing tools in structural biology, particularly for the examination of proteins with low propensity for crystallization.

Structural characterization of a protein adsorbed on aluminum hydroxide adjuvant in vaccine formulation

The heterogeneous composition of vaccine formulations and the relatively low concentration make the characterization of the protein antigens extremely challenging. Aluminum-containing adjuvants have been used to enhance the immune response of several antigens over the last 90 years and still remain the most commonly used. Here, we show that solid-state NMR and isotope labeling methods can be used to characterize the structural features of the protein antigen component of vaccines and to investigate the preservation of the folding state of proteins adsorbed on Alum hydroxide matrix, providing the way to identify the regions of the protein that are mainly affected by the presence of the inorganic matrix. l-Asparaginase from E. coli has been used as a pilot model of protein antigen. This methodology can find application in several steps of the vaccine development pipeline, from the antigen optimization, through the design of vaccine formulation, up to stability studies and manufacturing process.

Engineering l-asparaginase for spontaneous formation of calcium phosphate bioinspired microreactors

Active bioinspired materials are appealing biotechnological targets, and their study is gaining momentum. These materials, which comprise of an inorganic matrix and one or more biomolecules, are extremely variable and therefore may result difficult to characterize in their intimate structure. In this work we have prepared a hydroxyapatite-l-asparaginase composite, with the perspective of using it in acute leukemia treatment. We demonstrate that the use of electron microscopy and powder X-ray diffraction, combined with the atomic-resolution information coming from solid-state NMR, allows us to understand the topology of the material and how the different components interplay to obtain an active composite.

NMR of Macromolecular Assemblies and Machines at 1 GHz and Beyond: New Transformative Opportunities for Molecular Structural Biology

As a result of profound gains in sensitivity and resolution afforded by ultrahigh magnetic fields, transformative applications in the fields of structural biology and materials science are being realized. The development of dual low temperature superconducting (LTS)/high-temperature superconducting (HTS) magnets has enabled the achievement of magnetic fields above 1 GHz (23.5 T), which will open doors to an unprecedented new range of applications. In this contribution, we discuss the promise of ultrahigh field magnetic resonance. We highlight several methodological developments pertinent at high-magnetic fields including measurement of 1H-1H distances and 1H chemical shift anisotropy in the solid state as well as studies of quadrupolar nuclei such as 17O. Higher magnetic fields have advanced heteronuclear detection in solution NMR, valuable for applications including metabolomics and disordered proteins, as well as expanded use of proton detection in the solid state in conjunction with ultrafast magic angle spinning. We also present several recent applications to structural studies of the AP205 bacteriophage, the M2 channel from Influenza A, and biomaterials such as human bone. Gains in sensitivity and resolution from increased field strengths will enable advanced applications of NMR spectroscopy including in vivo studies of whole cells and intact virions.

Enriching the biological space of natural products and charting drug metabolites, through real time biotransformation monitoring: The NMR tube bioreactor

BACKGROUND

Natural products offer a wide range of biological activities, but they are not easily integrated in the drug discovery pipeline, because of their inherent scaffold intricacy and the associated complexity in their synthetic chemistry. Enzymes may be used to perform regioselective and stereoselective incorporation of functional groups in the natural product core, avoiding harsh reaction conditions, several protection/deprotection and purification steps.

METHODS

Herein, we developed a three step protocol carried out inside an NMR-tube. 1st-step: STD-NMR was used to predict the: i) capacity of natural products as enzyme substrates and ii) possible regioselectivity of the biotransformations. 2nd-step: The real-time formation of multiple-biotransformation products in the NMR-tube bioreactor was monitored in-situ. 3rd-step: STD-NMR was applied in the mixture of the biotransformed products to screen ligands for protein targets.

RESULTS

Herein, we developed a simple and time-effective process, the "NMR-tube bioreactor", that is able to: (i) predict which component of a mixture of natural products can be enzymatically transformed, (ii) monitor in situ the transformation efficacy and regioselectivity in crude extracts and multiple substrate biotransformations without fractionation and (iii) simultaneously screen for interactions of the biotransformation products with pharmaceutical protein targets.

CONCLUSIONS

We have developed a green, time-, and cost-effective process that provide a simple route from natural products to lead compounds for drug discovery.

GENERAL SIGNIFICANSE

This process can speed up the most crucial steps in the early drug discovery process, and reduce the chemical manipulations usually involved in the pipeline, improving the environmental compatibility.

High-Resolution Solid-State NMR Characterization of Ligand Binding to a Protein Immobilized in a Silica Matrix

Solid-state NMR is becoming a powerful tool to detect atomic-level structural features of biomolecules even when they are bound to (or trapped in) solid systems that lack long-range three-dimensional order. We here demonstrate that it is possible to probe protein-ligand interactions from a protein-based perspective also when the protein is entrapped in silica, thus translating into biomolecular solid-state NMR all of the considerations that are usually made to understand the chemical nature of the interaction of a protein with its ligands. This work provides a proof of concept that also immobilized enzymes can be used for protein-based NMR protein-ligand interactions for drug discovery.

Gd3+-chelated lipid accelerates solid-state NMR spectroscopy of seven-transmembrane proteins

Solid-state NMR (SSNMR) is an attractive technique for studying large membrane proteins in membrane-mimetic environments. However, SSNMR experiments often suffer from low efficiency, due to the inherent low sensitivity and the long recycle delays needed to recover the magnetization. Here we demonstrate that the incorporation of a small amount of a Gd³⁺-chelated lipid, Gd³⁺-DMPE-DTPA, into proteoliposomes greatly shortens the spin-lattice relaxation time (¹H-T ₁) of lipid-reconstituted membrane proteins and accelerates the data collection. This effect has been evaluated on a 30 kDa, seven-transmembrane protein, Leptosphaeria rhodopsin. With the Gd³⁺-chelated lipid, we can perform 2D SSNMR experiments 3 times faster than by diamagnetic control. By combining this paramagnetic relaxation-assisted data collection with non-uniform sampling, the 3D experimental times are reduced eightfold with respect to traditional 3D experiments on diamagnetic samples. A comparison between the paramagnetic relaxation enhancement (PRE) effects of Cu²⁺- and Gd³⁺-chelated lipids indicates the much higher relaxivity of the latter. Hence, a tenfold lower concentration is needed for Gd³⁺-chelated lipids to achieve comparable PRE effects to Cu²⁺-chelated lipids. In addition, Gd³⁺-chelated lipids neither alter the protein structures nor induce significant line-width broadening of the protein signals. This work is expected to be beneficial for structural and dynamic studies of large membrane proteins by SSNMR.

Solid state deuterium NMR study of LKα14 peptide aggregation in biosilica

In nature, organisms including diatoms, radiolaria, and marine sponges use proteins, long chain polyamines, and other organic molecules to regulate the assembly of complex silica-based structures. Here, the authors investigate structural features of small peptides, designed to mimic the silicifying activities of larger proteins found in natural systems. LKα14 (Ac-LKKLLKLLKKLLKL-C), an amphiphilic lysine/leucine repeat peptide with an α-helical secondary structure at polar/apolar interfaces, coprecipitates with silica to form nanospheres. Previous 13C magic angle spinning studies suggest that the tetrameric peptide bundles that LKα14 is known to form in solution may persist in the silica-complexed form, and may also function as catalysts and templates for silica formation. To further investigate LKα14 aggregation in silica, deuterium solid-state nuclear magnetic resonance (2H ssNMR) was used to establish how leucine side-chain dynamics differ in solid LKα14 peptides isolated from aqueous solution, from phosphate-buffered solution, and in the silica-precipitated states. Modeling the 2H ssNMR line shapes probed the mechanisms of peptide preaggregation and silica coprecipitation. The resulting NMR data indicates that the peptide bundles in silica preserve the hydrophobic interior that they display in the hydrated solid state. However, NMR data also indicate free motion of the leucine residues in silica, a condition that may result from structural deformation of the aggregates arising from interactions between the surface lysine side chains and the surrounding silica matrix.

Ubiquitin immobilized on mesoporous MCM41 silica surfaces - Analysis by solid-state NMR with biophysical and surface characterization

Deriving the conformation of adsorbed proteins is important in the assessment of their functional activity when immobilized. This has particularly important bearings on the design of contemporary and new encapsulated enzyme-based drugs, biosensors, and other bioanalytical devices. Solid-state nuclear magnetic resonance (NMR) measurements can expand our molecular view of proteins in this state and of the molecular interactions governing protein immobilization on popular biocompatible surfaces such as silica. Here, the authors study the immobilization of ubiquitin on the mesoporous silica MCM41 by NMR and other techniques. Protein molecules are shown to bind efficiently at pH 5 through electrostatic interactions to individual MCM41 particles, causing their agglutination. The strong attraction of ubiquitin to MCM41 surface is given molecular context through evidence of proximity of basic, carbonyl and polar groups on the protein to groups on the silica surface using NMR measurements. The immobilized protein exhibits broad peaks in two-dimensional 13C dipolar-assisted rotational resonance spectra, an indication of structural multiplicity. At the same time, cross-peaks related to Tyr and Phe sidechains are missing due to motional averaging. Overall, the favorable adsorption of ubiquitin to MCM41 is accompanied by conformational heterogeneity and by a major loss of motional degrees of freedom as inferred from the marked entropy decrease. Nevertheless, local motions of the aromatic rings are retained in the immobilized state.

(1)H-detected solid-state NMR of proteins entrapped in bioinspired silica: a new tool for biomaterials characterization

Proton-detection in solid-state NMR, enabled by high magnetic fields (>18 T) and fast magic angle spinning (>50 kHz), allows for the acquisition of traditional (1)H-(15)N experiments on systems that are too big to be observed in solution. Among those, proteins entrapped in a bioinspired silica matrix are an attractive target that is receiving a large share of attention. We demonstrate that (1)H-detected SSNMR provides a novel approach to the rapid assessment of structural integrity in proteins entrapped in bioinspired silica.

Biosilica-Entrapped Enzymes Studied by Using Dynamic Nuclear-Polarization-Enhanced High-Field NMR Spectroscopy

Enzymes are used as environmentally friendly catalysts in many industrial applications, and are frequently immobilized in a matrix to improve their chemical stability for long-term storage and reusability. Recently, it was shown that an atomic-level description of proteins immobilized in a biosilica matrix can be attained by examining their magic-angle spinning (MAS) NMR spectra. However, even though MAS NMR is an excellent tool for determining structure, it is severely hampered by sensitivity. In this work we provide the proof of principle that NMR characterization of biosilica-entrapped enzymes could be assisted by high-field dynamic nuclear polarization (DNP).

Silaffins in Silica Biomineralization and Biomimetic Silica Precipitation

Biomineralization processes leading to complex solid structures of inorganic material in biological systems are constantly gaining attention in biotechnology and biomedical research. An outstanding example for biomineral morphogenesis is the formation of highly elaborate, nano-patterned silica shells by diatoms. Among the organic macromolecules that have been closely linked to the tightly controlled precipitation of silica in diatoms, silaffins play an extraordinary role. These peptides typically occur as complex posttranslationally modified variants and are directly involved in the silica deposition process in diatoms. However, even in vitro silaffin-based peptides alone, with and without posttranslational modifications, can efficiently mediate biomimetic silica precipitation leading to silica material with different properties as well as with encapsulated cargo molecules of a large size range. In this review, the biomineralization process of silica in diatoms is summarized with a specific focus on silaffins and their in vitro silica precipitation properties. Applications in the area of bio- and nanotechnology as well as in diagnostics and therapy are discussed.

Differences in Dynamics between Crosslinked and Non-Crosslinked Hyaluronates Measured by using Fast Field-Cycling Relaxometry

The dynamic properties of water molecules in gels containing linear and crosslinked hyaluronic acid polymers are investigated by using an integrated approach that includes relaxometry, solid-state NMR spectroscopy, and scanning electron microscopy. A model-free analysis of field-dependent nuclear relaxation is applied to obtain information on mobility and the population of different pools of water molecules in the gels. Differences between linear and crosslinked hyaluronic acid polymers are observed, indicating that crosslinking increases both the fraction and the correlation time of water molecules with slow dynamics.

NMR of sedimented, fibrillized, silica-entrapped and microcrystalline (metallo)proteins

Resolution and sensitivity in solid state NMR (SSNMR) can rival the results achieved by solution NMR, and even outperform them in the case of large systems. However, several factors affect the spectral quality in SSNMR samples, and not all systems turn out to be equally amenable for this methodology. In this review we attempt at analyzing the causes of this variable behavior and at providing hints to increase the chances of experimental success.

Solid-state NMR studies of metal-free SOD1 fibrillar structures

Copper-zinc superoxide dismutase 1 (SOD1) is present in the protein aggregates deposited in motor neurons of amyotrophic lateral sclerosis (ALS) patients. ALS is a neurodegenerative disease that can be either sporadic (ca. 90%) or familial (fALS). The most widely studied forms of fALS are caused by mutations in the sequence of SOD1. Ex mortuo SOD1 aggregates are usually found to be amorphous. In vitro SOD1, in its immature reduced and apo state, forms fibrillar aggregates. Previous literature data have suggested that a monomeric SOD1 construct, lacking loops IV and VII, (apoSODΔIV-VII), shares the same fibrillization properties of apoSOD1, both proteins having the common structural feature of the central β-barrel. In this work, we show that structural information can be obtained at a site-specific level from solid-state NMR. The residues that are sequentially assignable are found to be located at the putative nucleation site for fibrillar species formation in apoSOD, as detected by other experimental techniques.

SedNMR: a web tool for optimizing sedimentation of macromolecular solutes for SSNMR

We have proposed solid state NMR (SSNMR) of sedimented solutes as a novel approach to sample preparation for biomolecular SSNMR without crystallization or other sample manipulations. The biomolecules are confined by high gravity--obtained by centrifugal forces either directly in a SSNMR rotor or in a ultracentrifugal device--into a hydrated non-crystalline solid suitable for SSNMR investigations. When gravity is removed, the sample reverts to solution and can be treated as any solution NMR sample. We here describe a simple web tool to calculate the relevant parameters for the success of the experiment.