Trends in Therapeutic Conjugates: Bench to Clinic

On the origin of the low immunogenicity and biosafety of a neutral α-helical polypeptide as an alternative to polyethylene glycol

Poly(ethylene glycol) (PEG) is a prominent synthetic polymer widely used in biomedicine. Despite its notable success, recent clinical evidence highlights concerns regarding the immunogenicity and adverse effects associated with PEG in PEGylated proteins and lipid nanoparticles. Previous studies have found a neutral helical polypeptide poly(γ-(2-(2-(2-methoxyethoxy)ethoxy)ethyl l-glutamate), namely L-P(EG3Glu), as a potential alternative to PEG, displaying lower immunogenicity. To comprehensively assess the immunogenicity, distribution, degradation, and biosafety of L-P(EG3Glu), herein, we employ assays including enzyme-linked immunosorbent assay, positron emission tomography-computed tomography, and fluorescent resonance energy transfer. Our investigations involve in vivo immune responses, biodistribution, and macrophage activation of interferon (IFN) conjugates tethered with helical L-P(EG3Glu) (L20k-IFN), random-coiled DL-P(EG3Glu) (DL20k-IFN), and PEG (PEG20k-IFN). Key findings encompass: minimal anti-IFN and anti-polymer antibodies elicited by L20k-IFN; length-dependent affinity of PEG to anti-PEG antibodies; accelerated clearance of DL20k-IFN and PEG20k-IFN linked to anti-IFN and anti-polymer IgG; complement activation for DL20k-IFN and PEG20k-IFN but not L20k-IFN; differential clearance with L20k-IFN kidney-based, and DL20k-IFN/PEG20k-IFN accumulation mainly in liver/spleen; enhanced macrophage activation by DL20k-IFN and PEG20k-IFN; L-P(EG3Glu) resistance to proteolysis; and safer repeated administrations of L-P(EG3Glu) in rats. Overall, this study offers comprehensive insights into the lower immunogenicity of L-P(EG3Glu) compared to DL-P(EG3Glu) and PEG, supporting its potential clinical use in protein conjugation and nanomedicines.

Synthesis, Hydrolytic Stability and In Vivo Biological Study of Bioconjugates of the Tetrapeptides FELL Containing Pyrrole Moiety

BACKGROUND

Bioconjugates are promising alternatives for the multiple targeting of any disease. Pyrrole heterocycle is well known with many activities and is a building block of a lot of medical drugs. On the other hand, peptides are short molecules with many advantages such as small size, ability to penetrate the cell membrane and bond-specific receptors, vectorizing potential, etc. Thus, hybrid molecules between peptide and pyrrole moiety could be a promising alternative as an anti-pain tool.

METHODS

New bioconjugates with a general formula Pyrrole (α-/β-acid)-FELL-OH (NH2) were synthesized using Fmoc/OtBu peptide synthesis on solid support. HPLC was used to monitor the purity of newly synthesized bioconjugates. Their structures were proven by electrospray ionization mass spectrometry. The Paw Pressure test (Randall-Selitto test) was used to examinate the analgesic activity. Hydrolytic stability of targeted structures was monitored in three model systems with pH 2.0, 7.4 and 9.0, including specific enzymes by means of the HPLC-UV method.

RESULTS

The obtained results reveal that all newly synthesized bioconjugates have analgesic activity according to the used test but free pyrrole acids have the best analgesic activity.

CONCLUSIONS

Although free pyrrole acids showed the best analgesic activity, they are the most unstable for hydrolysis. Combination with peptide structure leads to the hydrolytic stabilization of the bioconjugates, albeit with slightly reduced activity.

Development and Recent Advances in Lysine and N-Terminal Bioconjugation for Peptides and Proteins

The demand for creation of protein diversity and regulation of protein function through native protein modification and post-translational modification has ignited the development of selective chemical modification methods for peptides and proteins. Chemical bioconjugation offers selective functionalization providing bioconjugates with desired properties and functions for diverse applications in chemical biology, medicine, and biomaterials. The amino group existing at the lysine residue and N-terminus of peptides and proteins has been extensively studied in bioconjugation because of its good nucleophilicity and high surface exposure. Herein, we review the development of chemical methods for modification of the amino groups on lysine residue and N-terminus featuring excellent selectivity, mild reaction conditions, short reaction time, high conversion, biocompatibility, and preservation of protein integrity. This review is organized based on the chemoselectivity and site-selectivity of the chemical bioconjugation reagents to the amino acid residues aiming to provide guidance for the selection of appropriate bioconjugation methods.

Structural Investigation of Therapeutic Antibodies Using Hydroxyl Radical Protein Footprinting Methods

Commercial monoclonal antibodies are growing and important components of modern therapies against a multitude of human diseases. Well-known high-resolution structural methods such as protein crystallography are often used to characterize antibody structures and to determine paratope and/or epitope binding regions in order to refine antibody design. However, many standard structural techniques require specialized sample preparation that may perturb antibody structure or require high concentrations or other conditions that are far from the conditions conducive to the accurate determination of antigen binding or kinetics. We describe here in this minireview the relatively new method of hydroxyl radical protein footprinting, a solution-state method that can provide structural and kinetic information on antibodies or antibody-antigen interactions useful for therapeutic antibody design. We provide a brief history of hydroxyl radical footprinting, examples of current implementations, and recent advances in throughput and accessibility.

Advancing New Chemical Modalities into Clinical Studies

Drug discovery and development has experienced an incredible paradigm shift in the past two decades. What once was considered a predominant R&D landscape of small molecules within a prescribed properties and mechanism space now includes an innovative wave of new chemical modalities. Scientists in the pharmaceutical industry can now strategize across a variety of modalities to find the best option to modulate a given target and provide treatment for a specific disease. We have witnessed a remarkable change not only in molecular design but also in creative approaches to drug delivery that have enabled advancement of novel modalities to clinical studies. In this Microperspective, we evaluate the critical differences between traditional small molecules and beyond rule of 5 compounds, peptides, oligonucleotides, and biologics for advancing into development, particularly their pharmacokinetic profiles and drug delivery strategies.

Microfluidic Manufacture of Lipid-Based Nanomedicines

Nanoparticulate technologies have revolutionized drug delivery allowing for passive and active targeting, altered biodistribution, controlled drug release (temporospatial or triggered), enhanced stability, improved solubilization capacity, and a reduction in dose and adverse effects. However, their manufacture remains immature, and challenges exist on an industrial scale due to high batch-to-batch variability hindering their clinical translation. Lipid-based nanomedicines remain the most widely approved nanomedicines, and their current manufacturing methods remain discontinuous and face several problems such as high batch-to-batch variability affecting the critical quality attributes (CQAs) of the product, laborious multistep processes, need for an expert workforce, and not being easily amenable to industrial scale-up involving typically a complex process control. Several techniques have emerged in recent years for nanomedicine manufacture, but a paradigm shift occurred when microfluidic strategies able to mix fluids in channels with dimensions of tens of micrometers and small volumes of liquid reagents in a highly controlled manner to form nanoparticles with tunable and reproducible structure were employed. In this review, we summarize the recent advancements in the manufacturing of lipid-based nanomedicines using microfluidics with particular emphasis on the parameters that govern the control of CQAs of final nanomedicines. The impact of microfluidic environments on formation dynamics of nanomaterials, and the application of microdevices as platforms for nanomaterial screening are also discussed.

Bioanalytical Methods and Strategic Perspectives Addressing the Rising Complexity of Novel Bioconjugates and Delivery Routes for Biotherapeutics

In recent years, an increase in the discovery and development of biotherapeutics employing new modalities, such as bioconjugates or novel routes of delivery, has created bioanalytical challenges. The inherent complexity of conjugated molecular structures means that quantification of the bioconjugate and its multiple components is critical for preclinical/clinical studies to inform drug discovery and development. Moreover, bioconjugates involve additional multifactorial complexity because of the potential for in vivo catabolism and biotransformation, which may require thorough investigations in multiple biological matrices. Furthermore, excipients that enhance absorption are frequently evaluated and employed for the development of oral and inhaled biotherapeutics. Risk-benefit assessments are required for novel or existing excipients that utilize dosages above previously approved levels. Bioanalytical methods that can measure both excipients and potential drug metabolites in biological matrices are highly relevant to these emerging bioanalysis challenges. We discuss the bioanalytical strategies for analyzing bioconjugates such as antibody-drug conjugates and antibody-oligonucleotide conjugates and review recent advances in bioanalytical methods for the quantification and characterization of novel bioconjugates. We also discuss bioanalytical considerations for both biotherapeutics and excipients through novel administration routes and review analyses in various biological matrices, from the extensively studied serum or plasma to tissue biopsy in the context of preclinical and clinical studies from both technical and regulatory perspectives.

Designing Functional Bionanoconstructs for Effective In Vivo Targeting

The progress achieved over the last three decades in the field of bioconjugation has enabled the preparation of sophisticated nanomaterial–biomolecule conjugates, referred to herein as bionanoconstructs, for a multitude of applications including biosensing, diagnostics, and therapeutics. However, the development of bionanoconstructs for the active targeting of cells and cellular compartments, both in vitro and in vivo, is challenged by the lack of understanding of the mechanisms governing nanoscale recognition. In this review, we highlight fundamental obstacles in designing a successful bionanoconstruct, considering findings in the field of bionanointeractions. We argue that the biological recognition of bionanoconstructs is modulated not only by their molecular composition but also by the collective architecture presented upon their surface, and we discuss fundamental aspects of this surface architecture that are central to successful recognition, such as the mode of biomolecule conjugation and nanomaterial passivation. We also emphasize the need for thorough characterization of engineered bionanoconstructs and highlight the significance of population heterogeneity, which too presents a significant challenge in the interpretation of in vitro and in vivo results. Consideration of such issues together will better define the arena in which bioconjugation, in the future, will deliver functional and clinically relevant bionanoconstructs.

Lipid-Based Nanoparticles in the Clinic and Clinical Trials: From Cancer Nanomedicine to COVID-19 Vaccines

COVID-19 vaccines have been developed with unprecedented speed which would not have been possible without decades of fundamental research on delivery nanotechnology. Lipid-based nanoparticles have played a pivotal role in the successes of COVID-19 vaccines and many other nanomedicines, such as Doxil® and Onpattro®, and have therefore been considered as the frontrunner in nanoscale drug delivery systems. In this review, we aim to highlight the progress in the development of these lipid nanoparticles for various applications, ranging from cancer nanomedicines to COVID-19 vaccines. The lipid-based nanoparticles discussed in this review are liposomes, niosomes, transfersomes, solid lipid nanoparticles, and nanostructured lipid carriers. We particularly focus on the innovations that have obtained regulatory approval or that are in clinical trials. We also discuss the physicochemical properties required for specific applications, highlight the differences in requirements for the delivery of different cargos, and introduce current challenges that need further development. This review serves as a useful guideline for designing new lipid nanoparticles for both preventative and therapeutic vaccines including immunotherapies.

Automation and data-driven design of polymer therapeutics

Polymers are uniquely suited for drug delivery and biomaterial applications due to tunable structural parameters such as length, composition, architecture, and valency. To facilitate designs, researchers may explore combinatorial libraries in a high throughput fashion to correlate structure to function. However, traditional polymerization reactions including controlled living radical polymerization (CLRP) and ring-opening polymerization (ROP) require inert reaction conditions and extensive expertise to implement. With the advent of air-tolerance and automation, several polymerization techniques are now compatible with well plates and can be carried out at the benchtop, making high throughput synthesis and high throughput screening (HTS) possible. To avoid HTS pitfalls often described as "fishing expeditions," it is crucial to employ intelligent and big data approaches to maximize experimental efficiency. This is where the disruptive technologies of machine learning (ML) and artificial intelligence (AI) will likely play a role. In fact, ML and AI are already impacting small molecule drug discovery and showing signs of emerging in drug delivery. In this review, we present state-of-the-art research in drug delivery, gene delivery, antimicrobial polymers, and bioactive polymers alongside data-driven developments in drug design and organic synthesis. From this insight, important lessons are revealed for the polymer therapeutics community including the value of a closed loop design-build-test-learn workflow. This is an exciting time as researchers will gain the ability to fully explore the polymer structural landscape and establish quantitative structure-property relationships (QSPRs) with biological significance.

Folate Receptor-Mediated siRNA Delivery: Recent Developments and Future Directions for RNAi Therapeutics

RNA interference (RNAi), a gene regulatory process mediated by small interfering RNAs (siRNAs), has made remarkable progress as a potential therapeutic agent against various diseases. However, RNAi is associated with fundamental challenges such as poor systemic delivery and susceptibility to the nucleases. Targeting ligand-bound delivery vehicles has improved the accumulation of drug at the target site, which has resulted in high transfection efficiency and enhanced gene silencing. Recently, folate receptor (FR)-mediated targeted delivery of siRNAs has garnered attention due to their enhanced cellular uptake and high transfection efficiency toward tumor cells. Folic acid (FA), due to its small size, low immunogenicity, high in vivo stability, and high binding affinity toward FRs, has attracted much attention for targeted siRNA delivery. FRs are overexpressed in a large number of tumors, including ovarian, breast, kidney, and lung cancer cells. In this review, we discuss recent advances in FA-mediated siRNA delivery to treat cancers and inflammatory diseases. This review summarizes various FA-conjugated nanoparticle systems reported so far in the literature, including liposome, silica, metal, graphene, dendrimers, chitosan, organic copolymers, and RNA nanoparticles. This review will help in the design and development of potential delivery vehicles for siRNA drug targeting to tumor cells using an FR-mediated approach.

Molecular simulation of zwitterionic polypeptides on protecting glucagon-like peptide-1 (GLP-1)

Owing to their anti-fouling properties, zwitterionic polypeptides demonstrate great advantage on protecting protein drugs. When conjugated to glucagon-like peptide-1 (GLP-1), a drug for type-II diabetes, zwitterionic polypeptides confer better pharmacokinetics than uncharged counterparts. However, its microscopic mechanism is still unclear due to the complicated conformational space. To address this challenge, this work explored the interaction modes of GLP-1 with the unconnected repeat units, instead of the full-length polypeptides. The three repeat units are two zwitterionic pentapeptides VPKEG and VPREG, and one uncharged control VPGAG. Our molecular simulations revealed that the helical conformation of GLP-1 was stabilized by adding 40 polypeptides. Both VPGAG and VPREG formed dense packing shells around GLP-1, but the driving forces were hydrophobic and electrostatic interactions, respectively. In contrast, the packing shell composed of VPKEG was most loose, while could still stabilize GLP-1. The moderate electrostatic interactions endowed VPKEG an anti-fouling property, thereby avoiding non-specific interaction with other amino acids. The strong electrostatic interactions exerted by arginine promoted atomic contacts between VPREG and other residues, making it as "hydrophobic" as VPGAG. In summary, the combination of hydrophobic and moderate electrostatic interactions in VPKEG brings about a subtle balance between stabilizing GLP-1 and avoiding non-specific interaction.

Plasmonic gold nanostructures for biosensing and bioimaging

As one kind of noble metal nanostructures, the plasmonic gold nanostructures possess unique optical properties as well as good biocompatibility, satisfactory stability, and multiplex functionality. These distinctive advantages make the plasmonic gold nanostructures an ideal medium in developing methods for biosensing and bioimaging. In this review, the optical properties of the plasmonic gold nanostructures were firstly introduced, and then biosensing in vitro based on localized surface plasmon resonance, Rayleigh scattering, surface-enhanced fluorescence, and Raman scattering were summarized. Subsequently, application of the plasmonic gold nanostructures for in vivo bioimaging based on scattering, photothermal, and photoacoustic techniques  has been also briefly covered. At last, conclusions of the selected examples are presented and an outlook of this research topic is given.

Triple, Mutually Orthogonal Bioorthogonal Pairs through the Design of Electronically Activated Sulfamate-Containing Cycloalkynes

Interest in mutually exclusive pairs of bioorthogonal labeling reagents continues to drive the design of new compounds that are capable of fast and predictable reactions. The ability to easily modify S-, N-, and O-containing cyclooctynes (SNO-OCTs) enables electronic tuning of various SNO-OCTs to influence their cycloaddition rates with Type I-III dipoles. As opposed to optimizations based on just one specific dipole class, the electrophilicity of the alkynes in SNO-OCTs can be manipulated to achieve divergent reactivities and furnish mutually orthogonal dual ligation systems. Significant reaction rate enhancements of a difluorinated SNO-OCT derivative, as compared to the parent scaffold, were noted, with the second-order rate constant in cycloadditions with diazoacetamides exceeding 5.13 M-1 s-1. Computational and experimental studies were employed to inform the design of triple ligation systems that encompass three orthogonal reactivities. Finally, polar SNO-OCTs are rapidly internalized by mammalian cells and remain functional in the cytosol for live-cell labeling, highlighting their potential for diverse in vitro and in vivo applications.

The Product of Matrix Metalloproteinase Cleavage of Doxorubicin Conjugate for Anticancer Drug Delivery: Calorimetric, Spectroscopic, and Molecular Dynamics Studies on Peptide-Doxorubicin Binding to DNA

Matrix metalloproteinases (MMPs) are extracellular matrix degradation factors, promoting cancer progression. Hence, they could provide an enzyme-assisted delivery of doxorubicin (DOX) in cancer treatment. In the current study, the intercalation process of DOX and tetrapeptide–DOX, the product of the MMPs’ cleavage of carrier-linked DOX, into dsDNA was investigated using stationary and time-resolved fluorescence spectroscopy, UV-Vis spectrophotometry and isothermal titration calorimetry (ITC). The molecular dynamics (MD) simulations on the same tetrapeptide–DOX^…DNA and DOX^…DNA systems were also performed. The undertaken studies indicate that DOX and tetrapeptide–DOX can effectively bond with dsDNA through the intercalation mode; however, tetrapeptide–DOX forms less stable complexes than free DOX. Moreover, the obtained results demonstrate that the differences in DNA affinity of both forms of DOX can be attributed to different intercalation modes. Tetrapeptide–DOX shows a preference to intercalate into DNA through the major groove, whereas DOX does it through the minor one. In summary, we can conclude that the tetrapeptide–DOX intercalation to DNA is significant and that even the lack of non-specific proteases releasing DOX from the tetrapeptide conjugate, the presence of which is suggested by the literature for the efficient release of DOX, should not prevent the cytostatic action of the anthracycline.

Selective Modification of Tryptophan Residues in Peptides and Proteins Using a Biomimetic Electron Transfer Process

We report here a photochemical process for the selective modification of tryptophan (Trp) residues in peptides and small proteins using electron-responsive N-carbamoylpyridinium salts and UV-B light. Preliminary mechanistic experiments suggest that the photoconjugation process proceeds through photoinduced electron transfer (PET) between Trp and the pyridinium salt, followed by fragmentation of the pyridinium N-N bond and concomitant transfer of this group to Trp. The reaction displays excellent site selectivity for Trp and is tolerant to other, redox-active amino-acid residues. Moreover, the reaction proceeds in pure aqueous conditions without the requirement of organic cosolvents or photocatalysts, is enhanced by glutathione, and operates efficiently over a wide range of peptide concentrations (10-700 μM). The scope of the process was explored through the labeling of 6-Trp-containing peptides and proteins ranging from 1 to 14 kDa. We demonstrate the versatility of the N-carbamoylpyridinium salt both by tuning the electrochemical and photochemical properties of the pyridinium scaffold to enable challenging photoconjugation reactions and by using the carbamoyl moiety to tether a plethora of productive functional groups, including reactive handles, purification tags, and removable protecting groups.

A modular and orthogonally reactive platform for fabrication of polymer–drug conjugates for targeted delivery

Increasing interest in utilization of polymeric systems in targeted drug delivery has necessitated fabrication of polymers that undergo facile functionalization with targeting groups and therapeutic agents in a modular and orthogonal fashion.