Bioconjugated oligonucleotides: recent developments and thera-eutic applications
Sébastien Benizri, Arnaud Gissot, Andrew Martin, Brune Vialet, Mark Grinstaff, Philippe Barthélémy
Bioconjugated oligonucleotides: recent developments and therapeu-tic applications
Sebastien Benizri, §†‡
Arnaud Gissot, §†‡
Andrew Martin,
Brune Vialet, §†‡
Mark W. Grinstaff, * and Philippe Barthélémy* §†‡ § Inserm U1212, F-33076 Bordeaux, France, † CNRS 5320, F-33076 Bordeaux, France, ‡ Université de Bordeaux, 146 rue Léo Saignat, F-33076 Bordeaux Cedex, France,
Departments of Biomedical Engineering, Chemistry, and Medicine, Boston Uni-versity, Boston, 02215, Massachusetts, USA . KEYWORDS oligonucleotides, bioconjugates, mRNA, antisense DNA (ASO), RNA interference (RNAi).
ABSTRACT:
Oligonucleotide-based agents have the potential to treat or cure almost any disease, and are one of the key therapeutic drug classes of the future. Bioconjugated oligonucleotides, a subset of this class, are emerging from basic research and being suc-cessfully translated to the clinic. In this review, we first briefly describe two approaches for inhibiting specific genes using oligonu-cleotides - antisense DNA (ASO) and RNA interference (RNAi) – followed by a discussion on delivery to cells. We then summarize and analyze recent developments in bioconjugated oligonucleotides including those possessing GalNAc, cell penetrating peptides, α-tocopherol, aptamers, antibodies, cholesterol, squalene, fatty acids, or nucleolipids. These novel conjugates provide a means to en-hance tissue targeting, cell internalization, endosomal escape, target binding specificity, resistance to nucleases, and more. We next describe those bioconjugated oligonucleotides approved for patient use or in clinical trials. Finally, we summarize the state of the field, describe current limitations, and discuss future prospects. Bioconjugation chemistry is at the centerpiece of this therapeutic oligonucleotide revolution, and significant opportunities exist for development of new modification chemistries, for mechanistic studies at the chemical-biology interface, and for translating such agents to the clinic.
INTRODUCTION
The molecular biology central dogma describes the transfer of biological information stored in genes to proteins us-ing biomacromolecules. The biomacromolecule deoxyribonu-cleic acid (DNA) is found in all nucleated eukaryotic cells and it stores information via a specific sequence present in DNA. The first-step in this unidirectional process of genes to proteins is transcription whereby ribonucleic acid (RNA) is generated from DNA (i.e., transcription). RNA is then spliced into the nu-cleus to retain only the coding part of the RNA, namely the ex-ons. The resulting messenger RNA (mRNA) is transferred to the cytoplasm, where the ribosome reads the information and produces a protein (i.e., translation). These biomacromolecules play key roles in all aspects of life from life cycle, pathogenesis, to healing and, thus, opportunities exist to control a biological outcome by intervening in transcription or translation. In 1967, synthetic nucleoside derivatives were re-ported with the intent for specific base pairing with target se-quences . In 1978, Summerton developed methods for inacti-vating sequences through crosslinking , and Zamecnik and Ste-phenson reported that short synthetic DNA fragments (called oligodeoxynucleotides, ODN) from the Rous sarcoma virus, possessing sequence binding complementary to RNA mole-cules, inhibited viral replication. This seminal discovery docu-mented replication prevention of a viral RNA strain using a spe- cific ODN - today known as antisense treatment . Several stud-ies have also elucidated many of the molecular mechanisms un-derlying different human and animal pathologies. Thus, altering the expression of pathological genes, whether genetic or modi-fied by mutation, is of keen interest and technologies are being developed for such purposes. Antisense DNA (ASO) and RNA interference (RNAi) are two very promising technologies for inhibiting specific genes. The former utilizes a DNA fragment complementary to the target mRNA sequence. The latter approach, first described by R. Jorgensen and extensively studied by Andrew Z. Fire and Craig Mello, uses small interfering RNAs (siRNAs) to target the mRNA. Antisense oligonucleotides induce different inhibi-tion mechanisms, which can occur in the cytoplasm and in the nucleus (Figure 1). After transcription of the DNA into pre-messenger RNA, several post-transcriptional modifications are performed, including splicing, capping at the 5' end, or the pol-yadenylation of the 3' end. The mRNA is then translocated into the cytoplasm by exportins, where it is then translated into pro-teins by ribosomes. A synthetic oligonucleotide elicits its activ-ity in two cellular compartments, the cytoplasm or the nucleus. After hybridization of the oligonucleotide on mRNA, two in-hibitory mechanisms are possible: i) mRNA degradation or ii) translational repression. mRNA is degraded upon hybridization with an oligonucleotide following RNase H recognition. Anti-sense DNA can also inhibit the translation step via a steric hin- drance mechanism at the ribosome binding site or by prohibit-ing the ribosomal motion along the mRNA. Several mecha-nisms of inhibition are also possible in the nucleus, including the inhibition of post-transcriptional modifications, such as cap-ping at the 5' end, or by binding to polyadenylation sites at the 3' UTR ends.
Additionally, antisense may also inhibit or promote the inclusion of exons to alter the splicing of pre-mRNA (Figure 1). In principle, protein regulation is accomplished by the use of either agonist or antagonist strategies, with the caveat that the target RNA sequence is known. Because they are exogenous molecules, synthetic oligonucleotides are substrates for endo- and exo-nucleases, and thus exhibit short half-lives both in vitro and in vivo . For example, after intravenous (IV) injection in monkeys, phosphodiester oligonucleotide ana-logues are quickly degraded with a half-life of only 5 minutes. In order to overcome this low stability, oligonucleotides are chemically modified. Sites of chemical modification include the base, ribose, and the phosphate linkage. The types of modifica-tions vary from classical to non-classical bioisosteres. Addi-tionally, one chemical modifications does not always address the same half-life limitation(s), and often two or more modifi-cations are combined to increase oligonucleotide stability. Dur-ing the last few decades, many different modification chemis-tries have been developed (Figure 2). One of the first chemical modifications reported is the replacement of the phosphodiester by a phosphorothioate linkage (PTO) to minimize oligonucleo-tide degradation. Interestingly, this modification does not inter-fere with the recruitment of RNase H and target RNA cleavage. Structures of the different chemical modifications and the knockdown mechanisms are shown in Figure 2.
To improve the binding affinity and nuclease resistance, chemical modifi-cations including the 2’-O-methyl (2’-OMe), 2′-O-methoxy-ethyl (2′-MOE), and/or 2’-fluoro (2’-F) modifications of RNA are inserted into the structure. To enhance the binding affinity, Locked nucleic acid (LNA) modifications are used where the conformational freedom of the ribose is restricted. More re-cently, Tricyclo-DNA (tcDNA) are reported as another con-strained nucleotide featuring a three-ring scaffold. Importantly, these types of chemical modifications efficiently address the degradation issues. However, they do not improve the cellular uptake or targeting of the oligonucleotide to a specific site at the cellular, tissue, or organ level. Indeed, these hydrophilic poly-anions do not easily cross a physiologic barrier (e.g., skin) or a cell membrane.
Figure 1: Mechanisms of antisense oligonucleotides (adapted from Chan J. H. P. et al. ) Normal expression of the gene and protein in the absence of ASO (1). After internalization, ASO hybridize to mRNA via complementary sequence pairing. The ASO/mRNA heteroduplex induces activation of RNase H and de-gradation of the mRNA (2) or ribosome blockage by steric hin-drance (3). Both mechanisms result in inhibition of target protein production. Alternatively, penetration of ASO into the nucleus may lead to regulation of mRNA via inhibition of capping forma-tion at the 5’ end (4), inhibition of splicing (5) or the activation of RNase H (6). Figure 2: Chemical modifications of synthetic oligonucleotides (Adapted from Khvorova A. and Watts J. K. 2017 ) Chemical modifications are incorporated at the phosphate, ribose or at the 5’ or 3’ ends of the oligonucleotides. The type and the position of the modification induce three main mechanisms (steric blockers in green, activation of RNase H in blue and RNA interference (RNAi) in orange). In the case of 2’ modification (2’-OMe, 2’-O-MOE, 2’NH , 2’-F-RNA and 2’-F-ANA), RNase H and RNAi me-chanism are possible with a gapmer design. PTO: Phosphorothioate ; CNA : Dioxaphosphorinane-Constrai-ned Nucleic Acid ; PNA :
Peptide Nucleic Acid ; PMO : P hospho-rodiamidate Morpholino Oligonucleotide ; E-VP : (E)-
VinylPhos-phonate ; ddC : dideoxyCytosine ; 2’-OMe : 2’ O-Methyl ;2’-O-MOE : 2’-O-MethOxy Ethyl ; 2’-F RNA; 2’-F ANA :
ArabinoNu-cleic Acid ; LNA :
Locked Nucleic Acid ; ENA : ; cEt :
S-constrained Ethyl ; tcDNA : tricycloDNA ; FHNA :
Fluoro Hexitol Nucleic Acid ; UNA :
Unlocked Nucleic Acid . Therapies must adhere to a wide range of stringent specifications in order to advance into clinical trials and suc-ceed. An ideal oligonucleotide therapy is safe to administer, af-fordable to produce, exhibits a 2 year shelf-life, possesses an extended half-life in blood and serum (> 12 hrs), and inhibits intended targets effectively with low nonspecific or off-target interactions. That said, differing disease indications will re-quire fine tuning of the design requirements for optimal perfor-mance. As discussed below, a wide range of modifications to oligonucleotides improve one or many of these parameters, and the use of bioconjugation to oligonucleotides is primarily fo-cused on improving the delivery of oligonucleotides to the cy-tosol or nucleus. Bioconjugates address a number of different oligonucleotide delivery challenges, such as improving biodis-tribution to a specific region or cell type (e.g., antibodies), pro-moting endosomal escape (e.g., CPP), increasing receptor-me-diated transport (e.g., GalNAc), and/or increasing lipophilicity (e.g., cholesterol). In this review, we discuss recent advances in the de-livery of oligonucleotides. We briefly describe self-assembly approaches based on electrostatic, hydrophobic, or H-bonding interactions to give, for example, lipoplexes, and refer the reader to several comprehensive reviews on this topic.
We focus on modified bioconjugated oligonucleotides for delivery, including GalNAc, cell penetrating peptides, α-tocopherol, ap-tamers, antibodies, cholesterol, squalene, fatty acids, nucleoli-pids, and bis-conjugates. We also describe relevant linking chemistries between the oligonucleotide and the bioconjugate with respect to molecular design.. Additionally, the therapeutic applications of such bioconjugated oligonucleotides and out-comes from clinical trials are highlighted. Finally, we summa-rize the state of the field and discuss future prospects. Today, significant opportunities exist for development of new modifi-cation chemistries, for mechanistic studies at the chemical-biol-ogy interface, and for engineering systems for efficient delivery to the target site.
OLIGONUCLEOTIDE DELIVERY
Cellular uptake is one of the key steps in order for ol-igonucleotides to elicit their biological activity, as the target mRNAs and the cellular machinery are located in the cytoplasm and in the nucleus. Several transfection agents have been devel-oped and commercialized for the intracellular delivery of oligo-nucleotides such as oligofectamine 2000 (Invitrogen), JetPEI (Polyplus transfection) or K2 (Biontex). Many of these trans-fecting products are composed of cationic lipids, polyethyl-enimine, or DEAE-dextran, which self-organize and self-as-semble in aqueous medium via electrostatic interactions with the negatively charged oligonucleotides. This strategy com-pacts the oligonucleotide into aggregates for subsequent endo-cytosis by the cell. Once inside the cell, the oligonucleotides are released into the cytoplasm. However, toxicity remains a disad-vantage of these agents, as most of transfecting agents are cati-onic, but alternatives are being investigated.
Additionally, many of these complexes are not stable in the presence of se-rum, limiting or preventing their in vivo use.
Following in-travenous administration, the resultant oligonucleotide/trans-fecting agent complexes accumulate primarily in the liver, due to their size. Consequently, significant research efforts are dedicated to the delivery challenges in order to improve the transfection of nucleic acids.
For example, poly(2-dime- thylaminoethyl) methacrylate, when mixed with oligonucleo-tides, forms micelles of controlled sizes based on the N/P ra-tio. Upon adding an albumin coating to the surface, the cyto-toxic effect of the polymer is minimized and cancerous cells are preferentially transfected relative to healthy cells. Another strategy employs modified viruses, which internalize nucleic acids in cells.
However, this strategy can afford off-target toxicity since the oligonucleotides are not delivered in their syn-thetic form, but rather integrated into the viral genome. Lipid nanoparticles (LNP) are also being investigated as the non-viral transfecting cargo. However, the transfection efficiency is gen-erally lower than that observed for viral transfection systems. Recently, LNPs loaded with siRNA targeting Polo-Like Kinase 1 (PLK1) protein, present in the triple negative breast cancer cell line (MDA-MB-231), have been modified with antibodies to target tumors. Biodistribution studies of la-beled siRNA-LNPs demonstrated that antibody modified LNP (antibody against heparin-binding EGF-like growth factor, αHB-EGF) effectively delivered siRNA to tumor tissue in mice. Interestingly, the PLK1 protein expression was inhibited after intravenous injection of the LNPs and tumor growth was de-creased. These results indicate that antibody modified LNPs loaded with siRNA are a promising therapeutic approach for breast cancer. Another recent article investigated the biocon-jugation of antibodies to LNP for targeting endothelial cells lin-ing the vascular lumen.
These new particles were non toxic both in vitro and in vivo as well as preferentially accumulated in the lungs. In contrast, the same nanoparticles without conjugated anti-bodies quickly accumulated into the liver, indicating that targeting moieties (antibodies/LNP bioconjugate) can avoid the hepatic up-take with endogenous serum protein like Apo-E . Alternatively, bioinspired molecules such as nucleoli-pids (NL) are being used to construct LNPs. NLs self-assemble to form unique supramolecular structures, and the LNPs based NLs loaded with nucleic acids successfully transfect plas-mid DNA, siRNA, and antisense oligonucleotides to a number
Figure 3: Strategies for the delivery of ASO and/or siRNA. Adapted from Järver et al. 2012 A: Formation of a complex between a bio-molecule or a polymer and the oligonucleotide via electrostatic in-teractions and / or the hydrophobic effect, B: Formation of liposomal supramolecular structure with targeting or transfecting agent (PEG, peptide, CPP, protein, lipid glycoconjugate, etc.), C: Covalent con-jugation with the oligonucleotide by a stable or cleavable bond. of different cell lines: human breast adenocarcinoma MCF-7 cells, human liver (HepG2), mouse fibroblast (NIH 3T3), Chi-nese hamster ovarian (CHO) cells, and human prostate cancer (PC-3) cells.
Furthermore, these LNPs can be further modified to be stimuli-responsive, such as responding to changes in pH to enhance the delivery of nucleic acids. The above examples are representative and by no means compre-hensive, as there are many formulations described for nucleic acid vectorization (Figure 3), and the reader is referred to sev-eral comprehensive reviews on the subject.
The re-targeting of nucleic acids using viral vectors was investigated by Reynolds et al. in the 2000’s.
Viral vec-tors are attractive candidates for in vivo gene delivery because the infection efficacy is higher compared to other non-vial ap-proaches. For example an adenovirus vector was prepared con-taining both a Fab fragment of an anti-Ad5 knob antibody and the anti-ACE monoclonal antibody mAb 9B9. This bi-specific conjugate exhibited enhanced pulmonary distribution by a syn-ergic effect (transductional and transcriptional).
The major drawback of using this vector is sequestration by Kupffer cells into liver tissue.
BIOCONJUGATED OLIGONUCLEOTIDE DELIVERY
The conjugation of specific molecules to oligonucleo-tides is a promising therapeutic approach for nucleic acid based drugs. Consequently, bioconjugates are of increasing presence in the pharmaceutical development pipeline. The major ad-vantages of working with a bioconjugate include: 1) a new chemical entity; 2) of defined composition; and, 3) synthesized using chemical methods as opposed to bioprocesses. These at-tributes, unlike formulations with polymers or other transfect-ing reagents that give heterogeneous mixtures requiring ex-tensive multi-pronged characterization analyses, will facilitate translation to the clinic. Additionally, these covalently conju-gated molecules play one or more roles in recognition, targeting of cells or tissues, cellular internalization, and pharmacokinet-ics. The review of covalently conjugated oligonucleotides necessitates discussion on appropriate and effective linkers and linking chemistries, as interference strategies can be stymied by functionalization(s) . Both cleavable and stable linkers are suc-cessfully used. Bio-orthogonal “click” chemistry approaches such as akyne-azide, and thio-maleimide are two common ap-proaches to form stable linkages with highly specific reactions. Cleavable bonds such as reducible disulfide linkages, esters (cleavable through hydrolysis or esterases), phosphodiesters (cleavable through nucleases) and peptides (cleavable through proteases) are also being utilized and examples are discussed below. Additionally, alternatives such as end functionalization (5’ or 3’), and other cleavable strategies will be discussed in the context of different conjugated moieties. PEG modification.
Poly(ethylene glycol) (PEG) was first conjugated to oligonucleotides more than two decades ago by different academic groups, including Bonora, and Bur-covich in order to improve stability, avoid rapid degradation, and enhance cellular uptake. In 2003, Ji Hoon Jeong et al. de-scribed PEG attached to an antisense oligonucleotide sequence ( c-myb ) to afford a surrounding corona, which would prohibit interactions with plasma proteins and increase aqueous solubil-ity. Intracellular uptake is achieved due to the formation of a micellar system resulting from the combination of PEG conju- gates with fusogenic cationic peptides. These formulations ex-hibit higher antiproliferative activity against smooth muscle cells compared to the unconjugated c-myb antisense.
GalNAc modification.
The GalNAc (N-acetylgalac-tosamine) modification, introduced by Nair et al., lead to hy-drophilic glycoconjugates (Figure 4), increasing the cellular internalization in the liver due to binding to the ASialoGlyco-Protein Receptor (ASGPR). These lectin type C receptors are highly expressed on the plasma membrane of hepatocytes and both galactose and GalNAc are the preferred ligands for these receptors. After binding to ASGPR, the complex is quickly in-ternalized to form early endosomes via a clathrin dependent mechanism. As a result, ASGPR targeting conjugates are readily delivered to the liver through intraveneous injection.
Once inside the cell, the oligonucleotides must escape from the endosome intact to elicit their bioactivity. At neutral pH, the dissociation constant between these modified oligonu-cleotides and their receptor is very low (Kd in the nanomolar
Figure 4: Molecular structures of GalNAc based conjugates, adapted from Matsuda et al. 2015 Diagram showing an oligonucleotide coupled to GalNAc (left) and molecular structure (right). The trian-tennular GalNAc is represented in the upper part, the GalNAc incor-porated in sequence in the lower part.
Figure 5: Cellular internalisation of GalNAc oligonucleotide conju-gates, adapted from Alnylam. The GalNAc moiety is a ligand of the ASGPR receptors. The formation of the complex induces a clathrin-dependent endocytosis mechanism. Acidification dissociates the siRNA-releasing substrate / receptor complex (3) into the cytoplasm (4). RNAi-mediated degradation of the targeted mRNA mechanism (5). Inhibition of protein translation (6). ASGPR receptors are re-cycled in the plasma membrane (7). range), indicating a strong association with ASGPR receptors. Once inside the endosome, the acidic pH allows for dissociation of the ligand-receptor complex, resulting in the return of ASGPR to the membrane (Figure 5) and subsequent release of the ligand. The GalNAc modification facilitates cell internali-zation. Finally, the GalNAc modified oligonucleotides escape the endosome. To prepare these bioconjugates, the GalNAc modifi-cation is introduced into the oligonucleotide either during DNA synthesis as a non-nucleoside monomer or at the end of the oli-gonucleotide synthesis as a "triantennular" form (Figure 4). The synthesis of such oligonucleotide conjugates is compatible with standard automated solid phase synthesis, where the GalNac modification is attached either at the 3', 5' extremities or within the oligonucleotide sequence. The non-nucleoside monomer is attached through a phosphodiester linkage during oligonucle-otide synthesis as a synthetic phophoramidite. All of the differ-ent chemical modifications (2'-OMe, 2'-F, PTO), which can be inserted within the same sequence, are compatible with the Gal-Nac conjugation approach. Manoharan et al reported that these modifications improve the in vivo stability of siRNA−GalNAc conjugates. Interestingly, after subcutaneous injection, the siRNA−GalNAc conjugates distribute to the liver with subse-quent gene expression decrease of the targeted mRNA, thus en-abling this approach for treating a wide range of liver dis-eases.
The pharmacokinetics of GalNAc-siRNA conjugates were evaluated in monkeys and it was found that phos-phorothioate linkages in the 5’-region of siRNA−GalNAc strands minimally affect plasma pharmacokinetics but result in a greater liver exposure. This provides a prolonged duration of gene silencing due to improved metabolic stability. The tech-nology was also developed for ASOs targeting apolipoprotein with a successful improvement (10-fold) of inhibition effect in vivo. In this study, the active ASO is liberated only after in-ternalization into cells and not in the plasma, demonstrating that ASO-GalNac conjugates are a functional prodrug. Many Gal-NAc conjugated oligonucleotides are currently in preclinical and clinical trials. For example, Fitusiran is a siRNA de-veloped by Alnylam for the treatment of hemophilias. The col-laboration between Ionis and Akcea yielded ASO IONIS-APO (a) LRX for the treatment of hyperlipoproteinemia and cardio-vascular diseases. Additionally, two anti-miRNAs are being de-veloped by Regulus to treat viral diseases, such as hepatitis C (RG-101), and a third is being developed in collaboration with AstraZeneca for the treatment of type 2 diabetes (RG-125). Peptide Sequences: Cell Penetrating Peptide (CPP) and RGD.
CPPs are short peptidic sequences, generally not ex-ceeding thirty residues, which possess the ability to cross a cel-lular membrane and facilitate endosomal escape (Figure 6). CPP are classified into three categories: 1) protein-derived pep-tides; 2) chimeric peptides formed by the fusion of two natural sequences; and, 3) synthetic peptides based on structure/func-tion studies. These short peptides are ligands for specific re-ceptors that facilitate cell internalization by endocytosis and de-stabilization of endosomes compartments. For example, Lönn et al. speculated that the PTD/CPP-EED domains enhance cel-lular delivery by insertion of a hydrophobic patch into the lipid bilayer at a critical distance (18 bonds) from the delivery do-main. This resulting concentration in the endosome results in a strong localized membrane destabilization leading to enhanced escape into the cytoplasm. All CPPs do not exhibit the same penetration mechanism, membrane leakage rates, or toxicity. In 2007, a CPP ((RXR)4 (X = 6-aminohexanoic acid)) conjugated to a PMO oligomer was investigated. The CPP-PMO conju-gates did not show toxicity below a dose of 15 mg/kg after in-travenous injection (bolus). However at a dose of 30 mg/kg, an-imal body weight decreased while at a dose of 150 mg/kg, the animals were lethargic with elevated levels of creatinine. Blood biochemisty analysis of albumin, electrolytes, and bilirubin showed constant levels at all doses. A major design issue for these conjugates is the com-plexation between the anionic oligonucleotides and the cationic CPPs. In a previous review, Steven Dowdy focused on the po-tential use of CPP to deliver siRNA, and the reader is referred to this manuscript. The endocytosis-mediated uptake of such peptides depends on three important steps: cell association, in-ternalization, and finally endosomal escape. Dowdy et al . also discuss the array of different cargos that have been delivered by cationic PTDs/CPPs as well as cellular processes and biological responses that have been modulated. CPPs share many common features responsible for efficient activity including positive amino acids (arginine and lysine) and hydrophobic residues (tryptophan and phenylalanine).
Alternatively, non-ionic ol-igonucleotides (PMO, PNA, phosphoryl guanidine) are good candidates to bypass this charge-charge complexation require-ment. Such systems are used successfully for exon skipping.
Conventional formulations that carry oligonucleotides are composed of CPP via physical mixing, but the conjugation of these molecules to the oligonucleotide by a covalent bond pro-vides additional benefits. The chemical insertion of multiple peptides on the same oligonucleotide improves the sensitivity of the conjugate for its receptor. In the case of siRNA conju-gated to cyclic RGD, the internalization mechanism is achieved
Figure 6: CPP grafting strategy on siRNA. A: Noncleavable oligonucleotide CPP conjugate. B: Representation of the cleavable conjugate by reduction of the disulfide bridge: (1) Bioconjugate en-ters into the cell thanks to CPP. (2) Cleavage of the disulfide bridge allows detachment of the siRNA from the CPP moiety. (3) CPP enters into the nucleus. (4) siRNA elicits its inhibitory activity by an RNAi mechanism. Adapted with permission from Ye, J., Liu, E., Gong, J., Wang, J., Huang, Y., He, H., and Yang, V. C. (2017) High-Yield Synthesis of Monomeric LMWP(CPP)-SiRNA Covalent Conjugate for Effective Cytosolic Delivery of SiRNA.
Theranostics , 2495−2508. Copyright 2017, Ivyspring. by caveola-dependent endocytosis.
In another study, the bombesin peptide, coupled to the 5’ end of a splice-shifting ol-igonucleotide (SSO), corrects splicing of an aberrant intron. This fourteen amino acid peptide, which is a neurotransmitter acting on the G protein receptors, facilitates oligonucleotide de-livery to the nucleus of transfected prostate cancer PC3 cells. Ye et al. demonstrated that a 3’ CPP covalently conjugated to siRNA increased their intra cellular delivery (Figure 6). The report investigated CPPs with different conjugation chemistries with a PEG space, one cleavable disulfide linkage, and another through a thiol-maleimide coupling. The incorporation of a sta-ble versus cleavable linkage led to differences in knockdown and efficacy. The linear tripeptide RGD and its cyclic-RGD analogs are well known peptides for cell targeting. These peptide lig-ands bind αvβ3 integrins which are overexpressed in several cancers, including melanomas, ovarian cancer, and breast cancer as well as in metastasis. Grafting such ligands to ther-apeutic oligonucleotides provides a means for targeting and ef-ficient delivery. However, a drawback of using the RGD as a targeting moiety is that the αvβ3 integrin is expressed on many cell types as well as platelets, and, as such off-target effects and toxicities are of concern. Although this class of peptide-modi-fied bioconjugates is being actively investigated for the delivery of nucleic acid in vitro , positive results still remain to be con-firmed in vivo . Additionally, biodistribution and resistance to proteolytic degradation are not reported. α-Tocopherol . α-Tocopherol, commonly known as vitamin E, is used for the treatment of hypercholesterolemia. This liposoluble moiety is often coupled to oligonucleotides to facilitate cell membrane interactions. For example, Yutaro Asami et al. coupled tocopherol to a siRNA at the 5' end of the 29-nucleotide antisense strand for reducing apolipoprotein B (ApoB) levels. Improved inhibitory activity is observed relative to the parent cholesterol derivative. In fact, only 2 mg/kg is needed to significantly reduce ApoB mRNA in mouse liver af-ter intravenous injection. In similar conditions, the amount of cholesterol conjugate required to observe the same activity was 50 to 100 mg/kg. Additionally, α-tocopherol, coupled to an ASO, increases endogenous gene inhibition in a mouse liver compared to an unconjugated ASO . Simply conjugating to-copherol to the oligonucleotide structure did not induce an in-hibitory effect, and a spacer of several (4-7) Unlocked Nucleic Acids (UNA) was required between the oligonucleotide 5’ex-tremity and tocopherol to maintain biological activity. In this study, the oligonucleotides within the ASO selected were Gap-mers, oligonucleotides containing a mixture of chemically mod-ified nucleotides (LNA, 2’-O-MOE, for example) at each ex-tremities and a central sequence of DNA (the “gap”), allowing the RNase H cleavage after forming the mRNA/DNA comple-mentary heteroduplex. The UNA residues, on the spacer, are cleaved in the cell affording the ASO using the RNase H mech-anism for inhibition of mRNA. The inhibitory efficacy in-creased by 3.5 fold compared to the intravenous injection of non-conjugated oligonucleotides. Importantly, tocopherol im-proved the pharmacokinetics of ASO affording accumulation in the liver (9- -after injection at a dose of 3 mg/Kg for the conjugated and un-conjugated ASO, respectively), unlike the unconjugated ASO, which distributed primarily to the kidneys (1-2 μg/g and 12-16 μg/g were found in the kidneys 6 h after injection at a dose of 3 mg/Kg for conjugated and unconjugated ASO, respectively).
Aptamers.
Aptamers are oligonucleotide sequences (DNA or RNA) possessing a three-dimensional structure for bi-ological recognition. Using a method called SELEX (System-atic Evolution of Ligands by EXponential enrichment) specific oligonucleotides are identified that bind a target with high af-finity (K d in the range of nanomolar to picomolar). Sullenger et al. used this approach to select an aptamer capable of targeting the Prostate-Specific Membrane Antigen (PSMA) receptor at the surface of prostate cells. The designed RNA molecule con-tained both the aptamer and siRNA moieties. This chimeric ap-tamer-siRNA features a dsRNA (siRNA) motif that is a sub-strate for the intracellular Dicer enzyme, an endoribonuclease. As a proof of concept, LNCaP and PC-3 prostate cells were treated with the chimeric aptamer-siRNA containing a thera-peutic siRNA sequence that targets genes overexpressed in hu-man tumors (PLK1 and BCL2). Successful knockdown resulted in a decrease in cell proliferation and an increase in apoptosis. As a control, an aptamer chimera bearing two point mutations exhibited an absence of specificity for its target, indicating the specific binding between the aptamer and its receptor. In an-other study, a siRNA targeting the tat/rev viral genes was con-jugated via a short polynucleotide link to an aptamer that rec-ognizes the glycoprotein gp120 of the HIV viral envelope. This conjugate suppressed HIV infection in human cell lines and in humanized mouse models. Aptamer-siRNA chimeras are of significant interest and the reader is referred to a recent re-view summarizing the state-of-the-art.
The additional ad-vantages of such chimeras include lower production costs, low batch-to-batch variation, longer shelf-life and little-to-no im-munogenicity and toxicity compared to antibody conjugates (discussed below). Given that the three-dimensional structure is required for recognition and that aptamers are degraded by nucleases, significant research efforts are directed at modifying nucleo-tides to increase the stability without losing target recognition. There are several locations and types of modifications being in-vestigated including: the terminals of nucleic acids, the phos-phodiester linkage, the sugar ring and modifications on the ba-ses, as well as 3’ end capping with inverted thymidine and PEG conjugation.
Antibodies.
Monoclonal antibodies are known for their recognition properties of biological targets. In 2005 Lieberman et al. reported the use of a monoclonal antibody conjugate for the delivery of siRNA in order to inhibit the pro-tein production of HIV. The antibody was conjugated to the ASO oligonucleotide via a click reaction involving an azide-modified antibody and a cyclooctyne ASO. This strategy was further developed by Satake et al. to conjugate the anti-CD22 antibody to the MXD3 oligonucleotide. This oligonucleotide targets a dimeric protein (MXD3) associated with MYC, a tran-scription factor responsible for the survival of B cell precursor cells in acute lymphoblastic leukemia. The conjugate induces inactivation of the MXD3 protein responsible for apoptosis in vitro in leukemic cells as well as affords cytotoxicity in normal B cells but not in hematopoietic cells, including stem cells. The in vivo results are promising as only a dose of 0.2 mg/kg twice a week for 3 weeks is required to double survival (median 42.5 vs. 20.5 days). Based on these encouraging results, antibody-ASO conjugates are a new therapeutic option to decrease the doses and to favor the accumulation of ASOs at designated lo-cations. However, the selection of antibody or antibody frag-ment for targeting a specific cell type is challenging. For exam-ple, Genentech published an article describing the investigation of antibodies conjugated to ASO by a maleimide linkage, for targeting prostate carcinoma cells after systemic administra-tion.
This challenge is further complicated by the fact that the route of antigen internalization also affects silencing. Although antibody conjugates reach the intended target site, the subse-quent steps of cellular internalization and endosomal escape are also required for efficacy.
Cholesterol.
Lipid moieties, and particularly choles-terol derivatives, are often conjugated to oligonucleotides for delivery purposes (Figure 7). Oligonucleotides modified with cholesterol are recognized by high and low-density lipoproteins (HDL and LDL) in vivo and internalized via cholesterol binding receptors. After intravenous or intraperitoneal injection, these oligonucleotide conjugates escape renal clearance, thus greatly impacting their pharmacokinetics by extending the time that the nucleic acids remain in the plasma. A number of studies have demonstrated the advantage of coupling a cholesterol moiety to the oligonucleotide in order to reduce its renal clearance. Also, cholesterol conjugation increases cellular uptake of oligonucle-otides. Godeau et al. reported improved in vitro cellular inter-nalization of an oligonucleotide functionalized with cholesterol via a "click chemistry" approach. Additionally, these conjugates inhibited viral translation of hepatitis via an IRES blocking mechanism.
Additional studies in the KB-8-5 cell line showed that the cholesterol moiety allows endosomal escape without the use of any additional transfecting reagents. After 4 hours, the siRNA conjugates accumulate in the intercellular space. After 24 hours, the distribution became homogeneous with an accumulation of the oligonucleotides in the cytoplasm of the cells.
From a design perspective, the spacer between the ol-igonucleotide and cholesterol is crucial to maintain the biologi-cal activity. Directly grafting the cholesterol to the 5' oligonu-cleotide end reduced the inhibitory activity of the nucleic acids (siRNA or ASO).
In another study, ApoB was targeted to the liver after a daily intravenous injection of siRNA-choles-terol conjugates at a dose of 50 mg/kg.
Additionally, the Hun-tingtin protein was inhibited after a single intrastriatal injection of a cholesterol-coupled siRNA. These two examples demon-strate that siRNA-cholesterol conjugation improves the delivery into different cell types other than liver cells.
A photo-respon-sive cholesterol-siRNA conjugate (on both sense or antisense strands) is recently reported containing a photo-cleavable link-age (Figure 7) . The orthonitrobenzyl group photo-cleaves in response to 365 nm UV light to yield the native 5’ end. Three different cholesterol derivatives were prepared to inhibit 3 dif-ferent genes (2 exogenous, luciferase and GFP; and an endoge-nous, Eg5) in hepatocarcinoma HepG2 cells. In the absence of light, this conjugation allows the internalization of the am-phiphilic cholesterol-siRNA without inhibiting the target. In the presence of a light stimulus, the link between the cholesterol and the siRNA is cleaved, and the inhibitory activity of siRNA is introduced.
Cholesterol is conjugated to oligonucleotides at dif-ferent locations including the 5' or 3' end, as well as within the sequence. A recent study reported six constructs conjugated with cholesterol covalently bound either at the ends or after thy-midines within the sequence. The oligonucleotide selected was a Gapmer with 2 and 3 LNAs at both the 5' and 3’ ends, respec-tively. Higher in vitro activities are obtained when the choles-terol is inserted either at the 5' end or within the sequence.
In vivo , the cholesterol conjugates accumulate in the liver inde-pendent of the lipid conjugation location (3’, 5’-ends or within the sequence). Furthermore, a regular phosphodiester linkage exhibited superior in vivo performance in terms of biological activity (by a factor of 5) compared to the analog phosphorothi-oate as a link between the lipid and the ASO. Nakajima et al. suggests that the unmodified phosphate is cleaved in the liver freeing the non-conjugated ASO.
In 2007, Moschos et al. co-valently attached the cholesterol moiety to the oligonucleotide sequence via a disulfide linker that is cleaved under intracellular reductive conditions.
In this study, the authors suggest that conjugation to cholesterol extends but does not increase siRNA-mediated mRNA knockdown in the lung (MAP kinase mRNA in mouse lung).
Squalene.
Squalene is a triterpene molecule and bio-synthetic precursor of cholesterol found in plants and animals. Squalene is often conjugated to the 3'-end of the sense strand of siRNA via a thiol-maleimide coupling. Due to the resulting am-phiphilic character of the squalene-oligonucloetide conjugate, these conjugates spontaneously formed spherical assemblies of 165 ± 10 nm diameter with a zeta potential of −
26 mV in aque-ous media. These nanoparticles show enhanced oligonucleotide stability in the presence of serum and higher catalytic potency in vitro and in vivo against the targeted RET/PTC1 mRNA com-pared to the unmodified siRNA. Up to 70% inhibition of the tumor growth is observed after 19 days following intravenous injections of 2.5 mg/kg modified siRNA at day 0, 2, 4, 7 and 10.
Fatty acids.
Currently in clinical trial (phase 2) for the treatment of myelofibrosis, GRN163L is a telomerase targeting, antisense oligonucleotide of thio-phosphoramidate with a cova-lently linked palmitic acid at the 5'-end (Figure 8).
The palmitic acid moity is conjugated though a PTO linkage to the backbone of the ASO. Telomerase activity is up-regulated in numerous cancers and, thus, is a viable target for treatment. Te-lomere shortening and lower cell viability are observed after in-hibition of telomerase activity in cancer cell lines. The IC val-ues ranged from 50 to 200 nM for telomerase expression in 10 Figure 7: Molecular structure of a photocleavable cholesterol-con-jugated oligonucleotide, adapted from Yang J. et al.
Figure 8: Molecular structure of GRN163L. The lipid oligonucleotide GRN163L, 5’ – Palm – TAGGGTTAGACAA – NH – 3’, with a thio-phosphoramidate inter-nucleosidic linkage (top) and its structu-ral formula (down) from the Chemspider website. different pancreatic cell lines in the presence of GRN163. Te-lomerase reactivation and elongation are also observed when the antisense is no longer present, indicating that sequences tar-geting the RNA template region of telomerase are effective in-hibitors of telomerase. GRN163L is a potential adjuvant for cancer treatment as it halts the progression of the tumor by re-storing a normal, correct phenotype for the cancerous cells. The in vitro inhibition of telomerase activity by ASO is improved with the palmitoyle modification. An inhibition factor ranging from 1.4 to 39 is observed depending on the cell type (cervix, glioblastoma, hepatocarcinoma, lungs, melanoma, myeloma, ovary and prostate). In vivo efficacy (up to 56% inhi-bition of telomerase activity after 24h compared to the uncou-pled antisense or PBS) is also observed in a murine xenograft model following intravenous injection (50 mg/kg) in the ab-sence of any additional transfecting reagent.
Additionally, in-vestigations reveal a synergistic effect when GRN163L is co-administered with trastuzumab, a recombinant monoclonal an-tibody targeting HER2+ receptors in breast cancers.
The composition of the lipid (oleic vs palmitic acid in the lipid oli-gonucleotide conjugate) was also evaluated, but with no notice-able difference in efficacy.
Ketal nucleolipid conjugate.
Nucleolipids, first reported by our groups, are also being investigated.
For example, the ketal uridine phosphoramidite with two alkyl chains at the 2’ and the 3’ positions, anchors oligonucleotides to liposomal mem-branes . These lipid-oligonucleotides are amphiphilic with micellar aggregation properties that are used as a functional res-ervoir for hydrophobic drugs. The drug payload of the micelles is released in the presence of the oligonucleotides complemen-tary to the lipid-DNA conjugate.
Similarly modified ASOs are investigated for the treatment of prostate cancer.
An anti-sense strategy based on targeting the Translational Controlled Tumor Protein (TCTP) is described for the treatment of Castra-tion resistant prostate cancer (CRPC), a disease currently with a very low survival rate (median survival reported between 9 and 30 months).
TCTP is minimally expressed in healthy prostatic tissue, moderately in prostatic cancer cells, and over-expressed in CRPC cells. Therefore, designing an inhibitory se-quence is key for this promising strategy for the treatment of CRPC. An ASO sequence of 20 nucleotides with PTO back-bone was selected to impede TCTP expression. Normally, this ASO sequence requires the assistance of a vectorization agent such as oligofectamine to be efficient in vitro . The conjugation of the ASO with the ketal nucleolipid enables the inhibition of TCTP in the absence of transfecting agent in vitro and in vivo.
Bis-conjugates.
Multi-functionalized, bis-conjugated oligonucleotides are also being investigated. Tajik-Ahmadabad et al. designed an amphiphilic CPP-modified ASO (in the PMO series) capable of self-assembly. The ASO is functional-ized by coupling a 3-maleimidopropanoic acid moiety to the free secondary amine group at the 3’ end. This maleimido-PMO was purified by HPLC method. The fatty-acid modified peptide was prepared by coupling myristic anhydride at the N-terminus of the resin-bound ApoE. After deprotection and resin cleavage, the ApoE peptide with C-terminal cysteine was conjugated to the ASO by thiol-maleimide click reaction. The spontaneous self-assembly of this ASO occurs when myristic acid is cova-lently attached to the N-terminus of the peptide. The bis-conju-gated ASO inhibits exon 7 splicing of the pre-mRNA SMN2 gene, which is responsible for the pathology of spinal muscular atrophy. These amphiphilic species exhibit a 4-fold increase in potency relative to the CPP-ASO mono-conjugate. A similar approach is described by Wada et al., who used cholesterol and GalNac as modifiers at the 5'-end of an ASO targeting ApoB (Figure 9).
The conjugation was pre-pared using phosphoramidite chemistry, amenable to solid sup-port synthesis of oligonucleotides. The monovalent GalNAc phosphoramidite used was described earlier by Yamamoto et al.
Such a dual conjugation strategy reduces the renal biodis-tribution of the oligonucleotide. In that case, the cholesterol-conjugated ASO also possessed a 3-nucleotide-long linker with phosphodiester linkages susceptible to endonuclease hydrolysis in the targeted tissues or cells. Accumulation of the GalNac-modified ASO is low in the kidney just like the double 5'-mod-ified cholesterol-GalNAc ASO. Renal accumulation is five times lower when the ASO is modified at both extremities one with the lipid and the other with GalNAc. As expected, the Gal-Nac modified ASOs preferentially accumulate in the liver. Thus, the cholesterol–GalNAc dual strategy represents an ef-fective strategy for reducing the nephrotoxic potential of ASOs, while maintaining the gene silencing activity in the liver.
Spherical Nucleic Acids.
Spherical Nucleic Acids (SNAs) are a class of nucleic acid conjugates differentiated from other conjugates here through their three dimensional nanostructure . First developed by Chad Mirkin, this structure is composed of oriented single or double stranded nucleic acids in a dense spherical array (Figure 10). First generation SNAs possessed a gold nanoparticle core with Au-S linkages to the nucleic acids, and since then have been expanded to contain other cores for specific applications . SNA structures are ame-nable to further modification to contain targeting ligands such as antibodies , and immune agents such as antigens . SNAs can also be formed with RNA , modified backbones , and sugar modifications . SNAs exhibit increased nuclease re-sistance due to their structure and are readily endocytosed into cells without additional transfection making them an attrac-tive bioconjugate class to enhance delivery . Liposomal SNAs are formulated from 1,2-dioleoyl-sn-glycero-3-phos-phocholine and a tocopherol-oligonucleotide conjugate which contains a phosphodiester linkage and a PEG spacer (discussed in its own section above). Tocopherol-oligonucleotide conju-gates form micellar structures, but liposomal SNAs provide ad-ditional benefit . Liposomal SNA formulations are being eval-uated as a novel therapy for immune modulation
For example, SNAs are effective for both immune TLR agonism and inhibition through either target sequence dependent binding to TLR receptors or the receptor for mRNA translation . Receptor agonism strategies focus on agonism through TLRs, and the activity of the SNA conjugates is dependent on linker chemistry. SNA and tocopherol oligonu-cleotide conjugates show effective immune stimulation and tu-
Figure 9: Cholesterol and GalNAc coupled ASO, adapted from Wada F. et al.
TEG : Triethylene glycol ; GalNAc : N -acetylgalactosamine ; ASO : AntiSense Oligonucleotide mor growth reduction in vivo , and SNA formulations demon-strate the highest efficacy. In a recent publication , a mela-noma-specific peptide antigen was conjugated via three differ-ent linkers to a TLR9 agonizing oligonucleotide adjuvant. The complimentary oligonucleotide was conjugated to an antigen. Three different antigen-oligonucleotide linkages were evalu-ated: one stable (N-(β-maleimidopropyloxy) succinimide es-ter), one cleavable (succinimidyl 3-(2-pyridyldithio)propio-nate), and a traceless linkage (4-nitrophenyl 2-(2-pyridyl-dithio)ethyl carbonate). See Figure 10 for structural compari-son. The traceless linkage undergoes an internal cyclization in addition to a disulfide cleavage to yield the antigen’s native N-terminus. The choice of linker conjugation significantly influ-enced activity. The SNA formulations possessing the cleavable, traceless delivery linkage yielded the greatest T cell activation and proliferation. Importantly, these findings highlight the crit-ical role the linker plays. Moreover, they also demonstrate the potential for oligonucleotide conjugates to expand to new ap-plications and a few SNA formulations are progressing through preclinical into early clinical development (e.g., NCT03086278, Table 1 and discussion below). . OLIGONUCLEOTIDES THERAPEUTIC APPLICATION
As exemplified in the preceding sections, numerous oligonucle-otides have been investigated for a range of diseases. The ma-jority of these bioconjugated oligonucleotides are in preclinical studies (i.e., in vitro and small animal in vivo efficacy studies). Importantly, several formulations are regulatory approved and used in the clinic (Table 1). The data accumulated in Table 1 are from company web sites and the clinicaltrials.gov web re-source. The first regulatory approved oligonucleotide (in 1998 by the FDA and in 1999 by the EMA (
European Medicines Agency )) was for the treatment of cytomegalovirus retina, a vi-ral infection of the eye. If untreated, vision loss can occur in immune compromised patients. Specifically, Fomivirsen (Vitravene ® ) was developed by IONIS Pharmaceutical (ISIS at the time) in collaboration with Novartis Ophthalmics. This biomacromolecule, composed of 21 PTO nucleotides, is com-plementary to one viral mRNA. The posology consists of a weekly intravitreal injection of 165 µg of a Fomivirsen solution at 6.6 mg/mL.
The market authorization was withdrawn on July 30th 2002 at the request of the manufacturer for business reasons. Vitravene ® is still authorized in Switzerland and can be administered in the European Union upon specific request. Im-portantly, this success laid the foundation for a number of oli-gonucleotides being ushered into commercial development and the reader is referred to several reviews on this topic. As discussed in the introduction of this Review, the design of oligonucleotides for use in the clinic requires specific design considerations and optimizations other than improved delivery.
For enhanced in vivo efficacy, oligonucleotides containing chemical modifications such as 2’-O-MOE, 2’OMe, LNA and PMO are used to protect against degradation and in-crease target binding affinity. To date, the most common oligo-nucleotide modifications are PTO DNA and 2’-O-MOE. Addi-tionally, 2’OMe and LNA are used, but most of these oligonu-cleotides are still in phase 1 or 2 clinical trials.
As of 2010, all of the oligonucleotides approved by the FDA and in phase 3 clinical trials contain PTO linkages. The selection of oligonucleotide modifications de-fines the mechanism(s) of inhibition (Figure 2). The majority of oligonucleotides in phase 1 or 2 trial participate in an RNase H based inhibition mechanism, but are of more diverse chemical composition and functionalization. That said, the inhibition mechanisms available include intron-exon splicing, RNase H activation, or blockage of translation through steric hindrance. The following subsections are organized according to targeted disease with a discussion of the bioconjugated oligonucleotides used as well as their mechanism of action.
Bone Marrow disorders. (Myelofibrosis and myelo-dysplastic disorders). Myeleofibrosis is caused by the replace-ment of bone marrow with scar tissue. The resulting scarring leads to a reduction of red blood cell formation. Myelodysplas-tic syndrome is a type of cancer in the bone marrow. Risk fac-tors are genetic or caused by or arise during some cancer treat-ments. Imetelstat is a palmitoyl lipid oligonucleotide conjugate in clinic trials to treat these diseases. This 13 nucleotide-long ASO targets telomerase activity, using palmitate as the target-ing ligand, with thio-phospharamidite linkages including the linkage to the palmitate group (Figure 11). The drug has completed multiple phase II clinical tri-als for metastatic breast cancer and multiple myeloma cancers patients. The dose is limited by thrombocytopenia. Imetelstat (GRN163L) received a fast track status in October 2017 from the FDA for certain patients with a myelodysplastic syn-drome.
Hepatitis B.
Hepatitis B is a common liver infection. The genome of the hepatitis B virus (HBV) is an attractive tar-get because there are multiple sites on the HBV genome that can be targeted simultaneously. There are several conjugates in the pipeline for the treatment of this disease. For example, ARC-520 is an equimolar combination of two cholesterol con-jugated siRNAs, siHBV74 and siHBV77, targeting an 18 nucle-
Figure 10: Spherical Nucleic Acids. A. SNAs present nucleic acids in an outward facing spherical array. B. Oligonucleotide-tocopherol conjugates form SNAs with liposomal cores. C. Structure of linkage and tocopherol moiety. D. TLR agonizing oligonucleotides conjugated to tocopherol can be combined with antigens through a complimentary oligonucleotide and chemical conjugation through a linker. E. Different conjugate linkage chemistries explored. otide long sequence in the HBV genome. In addition to the siR-NAs, a GalNAc conjugated peptide is included as an excipient to aid in delivery and endosomal escape. A Phase trial I was completed in 2018, but the results have not been publicized as of September 2018. Other clinical trials with ARC-520 have been withdrawn/terminated, likely due to the difficulty in knocking down expression due to HBV DNA integrated into the host genome. Arrowhead Pharmaceuticals has a combined phase I/II clinical trial currently recruiting for ARO-HBV. Al-nylam terminated a phase I clinical trial using ALN-HBV01, a 23 nucleotide long, GalNAc conjugated, siRNA. This GalNAc conjugated siRNA incorporated numerous modifications for solubility and stability, including 2'-F, 2-OMe, with PS linkages only near the siRNA termini. The discontinuation is part of a new agreement with Vir Biotechnology to begin development on ALN-HBV02, also a GalNAc conjugate, citing reduced off target effects due to the incorporation of glycol nucleic acids (GNAs) in the backbone.
Hemophilia.
Hemophilia is a blood clotting disorder. Fitusiran (ALN-AT3sc) is a GalNAc conjugate targeting an-tithrombin currently entering phase III clinical trials. In a phase I study, the mean antithrombin (AT) knockdown was reported to be 59%. The study included 4 healthy volunteers (A) and 12 patients with severe hemophilia (B). In one hemophilia patient, a maximal knockdown of 86% was reported along with 114 days bleed free. This conjugate was administrated via subcuta-neous injection. First phase results showed the reduction of lev-els of the antithrombin protein and the restoration of the balance for the production of clotting factors in adult A and hemophilia B patients, after a single monthly injection. The second phase of the trial was suspended because one hemophilia A patient died due to a cerebral edema. The suspension of the clinical trial was lifted after the trial’s protocol was amended to better miti-gate risks. Alnylam and Sanofi are scheduled to conduct a phase 3 clinical trial in 2018/2019 with the ATLAS program, which will include patients with hemophilia A and B with or without inhibitors, and patients previously receiving on-demand or prophylactic therapy.
Psoriasis.
Psoriasis is a chronic skin disease where skin cells undergo a rapid cell cycle. SNAs are being developed to treat dermatologic indications such as mild to moderate Pso-riasis . Recently completed results from Phase I studies for IL17RA and TNFα protein targets are promising (Purdue Pharma). The SNAs are absorbed through the skin and deliver siRNAs into the epidermis providing effective knockdown of targets within keratinocytes with minimal immune response. Topical administration offers a local treatment option, which minimizes systemic off-target effects.
Cancer.
Cancer is the unwanted abnormal growth and invasion of cells in the body. Of the various treatment classes – surgery, radiation, chemotherapy, and immunotherapy – immu-notherapy is a particularly exciting one as it provides a means to use the immune system to fight the disease. For example, ac- tivation of Toll-like receptor 9 (TLR9) initiates a cascade of in-nate and adaptive immune responses including increased inter-feron gene expression. Increased interferon gene expression correlates with improved responses to programmed death 1 (PD-1) inhibition. Thus, patients who did not respond or stopped responding to anti–PD-1 therapy are potential candi-dates for combined TLR9 agonists and anti–PD-1 therapy. Ex-icure has successfully completed a Phase I trial of TLR9 ago-nizing SNAs administered subcutaneously in healthy volunteers (NCT03086278). A Phase Ib/II study is planned to study intra-tumorally delivered SNAs both alone and in combination with intravenously administered pembrolizumab, an antibody target-ing the PD-1 receptor. The target cohort is in patients that have not yet responded to anti-PD-1 or anti-PD-L1 therapies (NCT03684785).
Figure 11: Structure of the thio-phospharamidite based ASO with a telomerase activity. The targeting moiety (palmitate) has been inserted at the 3’ extremity.
Age-Related Macular Degeneration.
Age-related Macular Degeneration (ARMD) is the gradual worsening of vi-sion and eye health over time due to retina damage. The blurring or loss of vision associated with ARMD is characterized by the proliferation of blood vessels behind the retina. In "wet" macu-lar degeneration, neovascularization can worsen symptoms and is activated by Vascular Endothelial Growth Factor (VEGF) signaling. Macugen ® (Pegaptanib) is a 27-nucleobase aptamer Table 1.
Bioconjugate oligonucleotides in the clinic.
Name Target Linker Moiety stage Trial Reference
APOC-III-L-Rx apoC-III GalNAc3 ii recriuting NCT03385239 ARC-520 HBV Cholesterol multiple i/ii NCT01872065 DCR-PHXC-101 GO GalNAc i recruiting NCT03392896 FXI-LRx Factor XI 2'-MOE GalNAc i recruiting NCT03582462 Inclisiran (ALN-PCSSC) PCSK9 GalNAc multiple i/ii/iii NCT03397121 Macugen VEGF PEG Approved Zimura (Avacincaptad pegol) C5 PEG iib NCT03374670 Fovista (E10030) PGDF PEG terminated NCT01944839 Imetelstat Sodium (GRN163L) telomerase thio-phosphoramidite Palmitate ii NCT01731951 Revusiran (ALN-TTRSC) TTR-FAC GalNAc discontinued Fitusiran (ANL-AT3sc) antithrombin GalNAc iii recruiting NCT03549871 Cemdisiran (ALN-CC5) Complement C5 GalNAc ii recruiting NCT03303313 Givosiran (ALN-AS1) ALAS1 GalNAc iii active NCT03338816 Lumasiran (ALN-G01) GO GalNAc ii enrolling NCT03350451 ALN-HBV HBV GalNAc i terminated NCT02826018 ALN-AAT alpha-1antitrypsin PiZZ allele GalNAC i/ii terminated NCT02503683 RG-101 HCV GalNAc terminated ALN-TTRSC02 TTR GalNAc i completed NCT02797847 Akcea-APO(a)-L_rx apoC-III 2'-O-(2-methoxyethyl) GalNAc ii active NCT03070782 IONIS-AGT-LRx AGT 5-10-5 MOE gapmer GalNAc i completed NCT03101878 IONIS-ANGPTL3-LRx ANGPTL3 Phosphtiorate and Phos-phodiester GalNAc ii NCT03371355 IONIS-TMPRSS6-LRx TMPRSS6 GalNAc i NCT03165864 ARO-HBV HBV i/ii, recruiting NCT03365947 IONIS-PKK-LRx PKK i recruiting NCT03263507 IONIS-GHR-LRx GHR ii recruiting NCT03548415 IONIS-AZ4-2.5-LRx undisclosed i recruiting NCT03593785 AMG-890 cardiovascular dis-ease i recruiting NCT03626662 ARC-AAT AAT Cholesterol ii, withdrawn NCT02363946 AST 008 TLR9 Spherical Nucleic Acids i completed NCT03086278 AST 008 and Pembroli-zumab i TLR9 Spherical Nucleic Acids i planned NCT03684785 XCUR17 IL17RA and TNFα Spherical Nucleic Acids i completed targeting VEGF binding, and possesses a 3’-3’ deoxy-thymidine extremity and a 5’end with two branched polyeth-ylene glycol chains of 20 kDa. The 2’ positions are modified for nuclease resistance purposes by 2’OMe for bases purines and fluorinated pyrimidines (Figure 12). Importantly, the aptamer binds the heparin site of VEGF with a picomolar affinity. The FDA approved this aptamer for the treatment of "wet" or Age-Related Macular Degeneration. Specifically, Macugen ® , in-jected intravitreally, locally reduces the proliferation/ expansion of blood vessels and a lack of adverse events is still observed at a dose ten times higher than clinically used. The product is available in the form of pre filled syringes of 90 µL solution containing 0.3 mg of active substance. Several other drugs have been developed for the treat-ment of ARMD. In the EU, Lucentis ® (ranibizumab, Novartis), a monoclonal antibody fragment that targets VEGF, and Eylea ® (aflibercept, Bayer) a recombinant fusion protein that binds to VEGF-A, VEGF-B, and placental growth factor (PIGF) with higher affinity than their native receptors. Avastin ® (bevaci-zumab, Roche) is a humanized recombinant monoclonal anti-body that binds VEGF and competitively inhibits the binding between VEGF and Flt-1 and KDR. It adds to the list of Macugen ® competitors in the United States. The other nucleic acid treatment for ARMD is a modified siRNA called beva-siranib. It is a duplex of a 21-nt long RNA that targets VEGF. Bevasiranib has not been approved but shows efficacy when combined with Lucentis ® in clinical trials. The effects of bevasiranib appear only six weeks after the beginning of the treatment, but the combination of Lucentis ® /bevasiranib pro-vides better visual acuity than Lucentis ® alone. Hepatic Porphyrias.
These conditions are a combina-tion of rare diseases that all overlap in that they all feature the accumulation of porphyrins in the blood. The build-up of these proteins causes nervous or dermatological symptoms. Currently in an ongoing phase III clinical trial, Givosiran (ALN-AS1), is a GalNAc conjugate siRNA targeting aminovulinate synthase 1 (ALAS1) present in the liver. In a Phase I trial with 23 patients, 11 patients reported mild or moderate adverse events (AE) with 1 reporting an unrelated, severe AE of abdominal pain and an-other reported unrelated AE of bursitis. Common mild/moder-ate AEs of abdominal pain, diarrhea, nasopharyngitis, and hy-poesthesia, pruritus, and rash were noted, but were not serious enough to stop treatment. The product was injected by single or multiple subcutaneous injections and compared to an injection of sterile normal saline solution. The purpose of the next phase 1 trial was to evaluate the safety and tolerability of Givosiran (ALN-AS1) in Acute Intermittent Porphyria (AIP) patients as well as to characterize pharmacokinetics (PK) and pharmaco-dynamics (PD) of ALN-AS1 in AIP patients. The safety and efficacy of Givosiran was evaluated in 17 patients with acute AIP. The patients were initially monitored for three months and those who experienced one porphyria attack were eligible to re-ceive once monthly injections of 2.5 or 5.0 mg/kg Givosiran or placebo for six months. Durable inhibition of ALAS1 was ob-served after Givosiran treatment. The lower tested dose of 2.5 mg/kg reduced the annualized attack rate by 83% and afforded a reduction of 88% of hemin compared to the placebo. A larger dose did not produce any amelioration. In 2018, data showed that at 22 months of therapy, patients were still experiencing a robust beneficial effect from Givosiran.
Famyloid polyneuropathy . Familial Amyloid Poly-neuropathy (FAP) is a genetic autosomal dominant disorder re-sulting from a mutation of the TTR (transthyretin) gene, leading to TTR protein aggregation, which negatively affects the nerv-ous system. Oligonucleotide therapeutic agents designed for the treatment of FAP, also known as Transthyretin-related heredi-tary amyloidosis (ATTR), target the mRNA sequence of trans-thyretin (TTR) for degradation. Three formulations are in clin-ical trials to decrease expression of TTR: Inotersen (developed by Ionis and GSK), Onpattro (Patisiran developed by Alnylam), and Revusiran (developed in collaboration between Alnylam and Sanofi Genzyme).
These therapeutics (2 siRNAs -one be-ing a GalNac conjugate- and an ASO) are in phase 3 clinical trials. One study compared the inhibitory activity of Inotersen (ASO) and Patisiran (siRNA). Both treatments led to a 80% de-crease in TTR expression.
Inotersen (IONIS-TTR Rx ), is a 20-nucleotide long gapmer PTO ASO with 5 2’-O-MOE modi-fications at both extremities. The ASO targets pre-mRNA that is degraded following RNase H activity. Inotersen sodium is subcutaneously injected weekly at a dose of 300 mg (284 mg of inotersen). Of note, three cases (out of the 172 patients tested over 64 weeks) reported thrombocytopenia. Inotersen has re-ceived marketing authorization approval from the European Commission (EC) for the treatment of stage 1 or stage 2 poly-neuropathy in adult patients with hereditary transthyretin amy-loidosis (hATTR). Inotersen is commercialized under the name of Tegsedi™. Patisiran (ALN-TTR02, Onpattro™) is an advanced siRNA under development and is administered intravenously as lipidic nanoparticles (LNP) at noticeably low doses of 0.3 mg/kg every three weeks over an 18-month period. The most common adverse events observed in patients were periph-eral edema and infusion related reactions.
In August 2018, Patisiran received U.S. Food and Drug (FDA) approval for the treatment of the polyneuropathy of hereditary transthyretin-me-diated amyloidosis in adults. Regulatory filings in other mar-kets, including Japan, are planned. The European Commission also granted marketing authorization for Onpattro™ on August 30th, 2018. Revusiran. a GalNac siRNA conjugate administered subcutaneously, was previously undergoing phase 3 clinical tri-als. This molecule has two PTO linkages, 22 2’-OMe nucleo-tides, and another 22 modified residues with 2’F modifications. However, development was stopped due to numerous AEs lead-ing to deaths in phase 3 clinical studies. Causes of theses side
Figure 12: Secondary structure of Pegaptanib, active substance of Ma-cugen ® Adapted from Ng E. W. M. et al. effects have not been published but the high weekly dose of 500 mg was suspected.
Historic timeline of developments
There have been numerous developments over the past 50 years that have led to the clinical efficacy of oligonu-cleotides for treating diseases.
The timeline featuring signifi-cant accomplishments is presented in figure 12. ASOs were the first oligonucleotides to reach clinical trials and to receive reg-ulatory approval . Notably, this conjugated (pegylated) aptamer has been in use for more than 14 years. The development of siRNA therapeutics advanced significantly in the early 2000s and their first use in humans occurred in 2005 (bevasiranib). siRNA therapeutics that functioned as splicing modulators fol-lowed next in development and commercialization. Antagomirs (miRNA inhibitors) were developed in 2009 and were followed by miRNA mimetics in 2013. These two former classes of oli-gonucleotides utilize miRNAs to modulate the activity of a given gene. For example, Miravirsen sequesters microRNA-122 and is used for the treatment of chronic hepatitis C, whereas mimics of microARN-34a exhibit potentiated anti-tumor activity. Over 30 oncogenes are known to be inhibited by this microRNA.
6. FUTURE OPPORTUNITIES AND CONCLUSION
Several bioconjugated oligonucleotides are regulatory ap-proved and used in the clinic. These bioconjugates possess a carbohydrate (Patisiran), a polymer (Pegaptanib), or a lipid (Imetelstat - GRN163L, currently on fast track status) cova-lently linked to the oligonucleotides. A number of additional ones are in preclinical development as well as clinical studies (see Table 1.). The primary function of these added conjugates is to enhance targeting, facilitate vectorization, reduce oligonu-cleotide susceptibility to nuclease activity, eliminate or reduce need for toxic transfection agents, and generally improve phar-macological activity and efficacy. Increasing the therapeutic window and reducing the likelihood for adverse events is a top priority, and the use of conjugated oligonucleotides is an effec-tive approach. As discussed above, these conjugates are lipo-philic or a targeting moiety. Most of the therapies currently in late-stage develop-ment target the liver and liver associated diseases. This is largely due to the success of the GalNAc modification, and the fact that the liver is an efficient filter for the blood. Other highly efficient targeting moieties need to be developed to target other organs or tissues – lung, kidney, heart, bone marrow, brain, muscle, etc. Poor delivery to target sites necessitates higher doses, decreasing safety with greater chances of AEs. One strat-egy to reduce the severity of AEs is to modulate or knockdown the effect after administration. For example, a single subcutane-ous 3 mg/kg GalNAc-siRNA dose can be effectively reversed with a 0.1 mg/kg GalNAc oligonucleotide conjugate targeting the seed region of the incorporated siRNA strand . The result demonstrates both effective knockdown and return of TTR pro-tein levels in preclinical in vivo studies. The evolution of safe antidotes for oligonucleotide therapies, such as the REVERSIR strategy reported by Zlatev et al., poses benefits for safety and adoption into the clinic.
The possibility to finely control RNAi pharmacology is a desired feature for highly efficient nu-cleic based therapeutic treatments. At the molecular level, advances in oligonucleotide chemistry are providing new methods and site-specific reac-tions to modify oligonucleotides at the base, sugar, phosphate, or end groups. Additionally, natural bases can be substituted
Figure 13: Timeline for Key Advances in Therapeutic Oligonucleotides. Adapted from Lundin K. E. et al.
The various substitutions and the advances of chemical modifications are shown in yellow, main discoveries and technological achievements are noted in blue and clinical studies are highlighted in green. with synthetic analogs. These developments afford a large di-versity of new and unique biomacromolecules. Still, significant opportunities exist in this area to improve on reaction effi-ciency, to expand on the compositional diversity of modifica-tions, and to realize structure-property relationships for na-noscale, self-assembling, and supramolecular systems. These improvements will allow for more modular, diverse, and effec-tive formulations. Similarly, molecular biology studies are providing new therapeutic targets with an improved under-standing of pathways and resulting pathologies. As such, the development of combination therapies is forthcoming. The pos-sible combinations will target either one or multiple mRNAs or combine a bioconjugated oligonucleotide with a small molecule or protein in order to improve efficacy and safety profiles. As discussed in this review, modifications such as GalNAc, cell penetrating peptides, α-tocopherol, aptamers, an-tibodies, cholesterol, squalene, fatty acids, and nucleolipids are new promising therapeutic candidates in the field. Despite the clinical progress to date, the design of modified oligonucleo-tides encompassing both the optimal delivery and efficient bio-logical activity remains an important challenge. Diseases such as coronary heart disease, lower respiratory infections, cancer, diabetes, and Alzheimer’s are in need of new therapies, and, as oligonucleotides can target and bind nearly any expressed mRNA, the possibility to develop oligonucleotide therapeutics exist. Key to these future successes will be understanding the pharmacokinetic and biodistribution profiles of these new ther-apeutics. Despite the promising bioconjugated oligonucleotides reported so far, oligonucleotide delivery represents a major hur-dle still to be addressed. As mentioned previously, most of the oligonucleotide conjugates used in clinic bio-accumulate in the liver. Furthermore, a clear relationship between the composi-tion and structure of the chemical modification and its resulting effect on pharmacokinetic/biodistribution must be both quanti-fied and established with appropriate positive and negative con-trols in place. For example, membrane interacting bioconju-gates often interact with many targets and are known for their promiscuity. Such a molecular rationale would allow scientists to design the chemical structure of the oligonucleotides depend-ing on the specific disease, target tissue/organ, cell type etc. In summary, the use of oligonucleotides in the clinic is in its infancy and the potential for significant advances in pa-tient care exist. Given the clinical success of monoclonical an-tibodies (mAb) as a biologic, we speculate that oligonucleotides will have a greater impact due to the specificity inherent to the target sequence, the ability to target nearly any protein, and their stability both pre-administration and in vivo . The full realization and maturation of the bioconjugated oligonucleotide therapeu-tic field will require time – e.g., 19 mAb drugs were on the mar-ket only after 20 years of development – but this should not cur-tail enthusiasm. In fact, findings from these mAb studies as well as from polymer conjugated enzymes and small molecules used in the clinic will catalyze development and subsequent clinical applicability.
Bioconjugation chemistry is at the centerpiece on this therapeutic oligonucleotide revolution. We encourage all to investigate this area where conceptualizing, designing, and engineering at the molecular level new functionalized oli-gonucleotides is key to success in the clinic.
AUTHOR INFORMATION
Corresponding Author * Mark W. Grinstaff, [email protected] * Philippe Barthélémy, [email protected]
ACKNOWLEDGMENT
This work was supported in part by funding from the Inserm trans-fert (IT), the National Institute of Health T32 Grant entitled Trans-lational Research in Biomaterials (NIH T32EB006359, AM), and the Distinguished Professor of Translational Research Chair at Boston University (MWG). The authors (PB and SB) thank Dr Lara Moumne (IT) for fruitful discussions.
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