AAV capsid design: A Goldilocks challenge

In the decades since the discovery of adeno-associated viruses (AAVs), efforts have been devoted to decoding its biology, the capsid 3D framework of major serotypes, and hundreds of natural isolates while accumulating an extensive structural database, a vast source for capsid remodeling. The logical progression of these efforts is now shifting from rational to combinatorial methods of engineering whereby next-generation sequencing analysis and in silico methodologies lead to discovery of new AAV genes, cellular pathways, and phylogeny. While limited for the time being, studies using machine learning for capsid design hold the promise of engineering AAV vectors that are more efficient, safe, and enduring. In vivo therapeutic gene transfer has emerged as a novel class of medicines. Its feasibility relies on the safe and efficacious delivery of genetic cargo to the appropriate targets. The adeno-associated virus (AAV) vector manifested itself as a preferred gene delivery vehicle enabling therapeutic gene expression for several clinical indications. Here, we cover the recent trends in AAV capsid engineering to enhance its targeting specificity, safety, and endurance. While each and every desirable trait can be individually remodeled, combining several attributes in one capsid amounts to a significant engineering challenge. Taking advantage of virion structure and phylogenetics, harnessing directed evolution, sequence analyses, and machine learning, researchers develop novel capsid variants to realize the goals of safe and enduring gene therapy. In vivo therapeutic gene transfer has emerged as a novel class of medicines. Its feasibility relies on the safe and efficacious delivery of genetic cargo to the appropriate targets. The adeno-associated virus (AAV) vector manifested itself as a preferred gene delivery vehicle enabling therapeutic gene expression for several clinical indications. Here, we cover the recent trends in AAV capsid engineering to enhance its targeting specificity, safety, and endurance. While each and every desirable trait can be individually remodeled, combining several attributes in one capsid amounts to a significant engineering challenge. Taking advantage of virion structure and phylogenetics, harnessing directed evolution, sequence analyses, and machine learning, researchers develop novel capsid variants to realize the goals of safe and enduring gene therapy. an attribute describing a viral capsid's propensity to attach to a specific cell surface receptor/s. a structural attribute of a virus to be recognized by and interact with a set of specific antibodies. the measure of overall or accumulated strength of a protein–protein interaction, sometimes related to a virus binding to primary and secondary receptor/s. groups of viruses evolved from the common ancestor, one branch (monophylum) on a tree of life. a method used in protein engineering that mimics the process of natural selection to steer proteins or nucleic acids toward a user-defined goal. It consists of subjecting a gene to iterative rounds of mutagenesis (creating a library of variants), selection (expressing those variants and isolating members with the desired function), and amplification (generating a template for the next round). a circumstance where the expression of one gene is affected by the expression of one or more independently inherited genes. Epistatic mutation refers to a genetic modification resulting in a trait observable only through the interaction with another mutation/s. genetic remnant of a virus that integrated into the host genome millions of years ago and is retained as a heritable element passed on to offspring until the present day. the first woman, a biblical figure. contiguous or nonlinear AA sequence on a capsid surface that antibodies or cell surface receptors recognize and bind to. a set of DNA variations, or polymorphisms, that tend to be inherited together. A haplotype can refer to a combination of alleles or to a set of SNPs found on the same chromosome. a type of antibody representing ~75% of serum antibodies in humans. a consensus mRNA sequence (GCC)RCCAUGG for initiation of translation in vertebrates, where R is a purine (A or G); the initiation codon is underlined. a protocol for deep sequencing analysis of DNA. a DNA or RNA sequence encoding the protein. Evolutionarily and structurally related viruses distinguished by their immune-reactive attributes. also known as DNA family shuffling or molecular breeding, a method of in vitro random recombination of homologous genes to generate mutant (shuffled) genes for directed evolution and to enable a rapid increase in DNA library size. relates to the mathematical concept describing a unit set of exactly one element. a productive infection of a cell. For rAAV, the term relates to the expression of a transgene. a protocol of introduction of foreign DNA into the cell. a propensity of a virus to infect a subset of particular cell types.