Nucleic acid drugs: recent progress and future perspectives

Abstract

High efficacy, selectivity and cellular targeting of therapeutic agents has been an active area of investigation for decades. Currently, most clinically approved therapeutics are small molecules or protein/antibody biologics. Targeted action of small molecule drugs remains a challenge in medicine. In addition, many diseases are considered 'undruggable' using standard biomacromolecules. Many of these challenges however, can be addressed using nucleic therapeutics. Nucleic acid drugs (NADs) are a new generation of gene-editing modalities characterized by their high efficiency and rapid development, which have become an active research topic in new drug development field. However, many factors, including their low stability, short half-life, high immunogenicity, tissue targeting, cellular uptake, and endosomal escape, hamper the delivery and clinical application of NADs. Scientists have used chemical modification techniques to improve the physicochemical properties of NADs. In contrast, modified NADs typically require carriers to enter target cells and reach specific intracellular locations. Multiple delivery approaches have been developed to effectively improve intracellular delivery and the in vivo bioavailability of NADs. Several NADs have entered the clinical trial recently, and some have been approved for therapeutic use in different fields. This review summarizes NADs development and evolution and introduces NADs classifications and general delivery strategies, highlighting their success in clinical applications. Additionally, this review discusses the limitations and potential future applications of NADs as gene therapy candidates.

Fig. 1

Historical timeline of essential discoveries in fundamental molecular biology theory and critical developments in NADs therapy. The orange boxes represent major biological discoveries in nucleic acids development, including the discovery of DNA and RNA, as well as researchers’ exploration of special biological phenomena such as RNA interference, nucleic acid hybridization, and gene editing. The yellow boxes show the breakthrough progress in the clinical application of NADs based on the aforementioned biological phenomena. These include successful clinical application cases of NADs, such as the first ASO drug Fomivirsen, the first siRNA drug Patisiran, the first aptamer drug Pegaptanib, the COVID-19 mRNA vaccines, as well as clinical trials for NADs in development, such as the saRNA drug MTL-CEBPA

Fig. 2

Classification and therapeutic mechanisms of NADs. a Gapmer ASO (consisting of a DNA-based internal gap with RNA-like flanking regions) binds to target mRNA with high affinity to form an RNA-DNA duplex and participates in RNase H-mediated mRNA degradation. b Steric block ASO regulates functional target gene expression through exon skipping or exon inclusion or interrupts translation initiation by targeting and masking the AUG start codon of the target mRNA. c siRNAs form RISC with AGO2. While the passenger strand is discarded, the antisense strand binds to the target mRNA, downregulating the translation level of the target mRNA. d pri-miRNAs produced by miRNA gene transcription in the non-coding region are processed to form mature miRNAs with the help of a series of complexes (Drosha/DGCR8, Exportin-5/RAN-GTP, and Dicer/TRBP). miRNAs combine with the AGO2 to form miRISC. The activity of miRNAs can be inhibited by miRNA inhibitors that either form a complex with the mature miRNA loaded in the miRISC complex or by masking a target site via interactions with the specific transcript being targeted. e saRNAs recruit the RITA complex (including AGO2, CTR9, RHA, and RNAP II) to stimulate the initiation and extension of transcription. f CRISPR-mediated gene editing mainly uses Cas9 and sgRNA to introduce DSBs at specific positions in the genome effectively. DSBs are generally repaired by HDR or NHEJ, achieving insertion, knockout, and site-specific mutagenesis. g Aptamers screened by SELEX technology can recognize specific proteins by forming 3D structures. h Exogenous mRNAs introduced into cells undergo translation to proteins and facilitate protein function through protein replacement therapy and mRNA vaccines

Fig. 3

Current challenges in NADs delivery. NADs are administered in many ways, such as intravitreal, intramuscular, intrathecal, and intravenous injection. For systemic delivery, NADs must first overcome renal clearance, nuclease degradation, immune system recognition, and drug off-target until reaching target tissues and organs. Subsequently, NADs successfully reach the target cells, enter the cell via endocytosis, enter the endosomes, and escape successfully to achieve the desired therapeutic effect. It is difficult for negatively charged NADs to cross the phospholipid bilayer on the surface of the cell membrane, which usually requires the help of carriers to recognize receptors or chemical modification of NADs to change properties

Fig. 4

Chemical structure of NADs delivery systems. a There are four types of LNPs: ILs (or CLs), auxiliary lipids, cholesterol, and PEGylated lipids. b Schematic and molecular structural formula of cationic polymeric nanoparticles. c Triantennary GalNAc moiety conjugated to siRNA or ASO. d Engineered exosome with RVG-LAMP2B displayed on the outer surface. The exosome contains therapeutic nucleic acids, such as siRNA, microRNA, and ASO. e Schematic of inorganic nanoparticles. f Peptide-assisted NADs delivery strategies. The methods of covalent conjugation include disulfide, amide, maleimide, thiazolidine, oxime, and thioether bond. The methods of non-covalent complexation include hydrophobic and electrostatic interactions

Fig. 5

Schematic of peptide-assisted NADs delivery. a Classes of peptides facilitating the delivery of NADs across biological barriers. b Classes of NADs. c The delivery methods of peptide-based carriers include peptide–oligonucleotide conjugates, peptide-based nanoparticles, and peptides in combination with other delivery systems. d Peptides mediate the entry of NADs into cells and transfer them across the cell membrane, complete endosomal escape, and eventually release NADs in the cytoplasm, mitochondrion, nucleus, endoplasmic reticulum, lysosomes, and Golgi apparatus

Fig. 6

Clinical application of NADs. Several NADs have been adopted as vaccines for treating rare genetic diseases, cancer, ophthalmic diseases, cardiovascular diseases, and infection diseases, and they have shown remarkable therapeutic effects. The box summarizes the therapeutic NADs for various diseases in the clinic or on the market