Analysis of hydrophobic and hydrophilic moments of short penetrating peptides for enhancing mitochondrial localization: prediction and validation

Abstract

Pharmaceutical interest in targeting mitochondria is increasing because of their contribution in incurable diseases. However, the inner mitochondrial layer represents a major hurdle to overcome for most drugs. Penetrating peptides are a promising strategy for drug delivery, but the absence of standard principles and reliable prediction tools limits the design and discovery of sequences with improved organelle specificity. In our hypothesis, peptide local flexibility represents a valuable source to predict peptide performance. Here, a pool of short nonnatural peptides was designed with the same amino acid content but different positioning. Molecular dynamics and membrane‐transfer simulations were used to generate the low‐energy conformers in extra, intracellular, and membrane‐inserted environments. The contributions of the hydrophobic and hydrophilic side chain–exposed surfaces revealed that the amino acid's relative position significantly affected the simulated peptide's dynamics. Based on the structural versatility, we predicted the peptides' behavior and the sequence with the most efficient membrane penetration and mitochondrial localization. The prediction and the improved performance of our peptides were experimentally confirmed and compared with a reported mitochondrial‐targeting sequence. We demonstrated that an accurate understanding of the structural versatility is a valid aid for future works in designing sequences with improved mitochondrial targeting.—Pirisinu, M., Blasco, P., Tian, X., Sen, Y., Bode, A. M., Liu, K., Dong, Z. Analysis of hydrophobic and hydrophilic moments of short penetrating peptides for enhancing mitochondrial localization: prediction and validation. FASEB J. 33, 7970–7984 (2019). http://www.fasebj.org

Prediction of Amphiphilic Cell-Penetrating Peptide Building Blocks from Protein-Derived Amino Acid Sequences for Engineering of Drug Delivery Nanoassemblies

“…Cell penetrating peptides (CPP) are short sequences of amino acids (generally up to 35 aa), which have a capacity to cross the cellular bilayer membranes without damaging them. [50][51][52][53][54][55][56][57][58][59][60] The research on CPPs has been inspired by the fact that proteins (like transcription-activating factors, signal sequences and homeoproteins) involve subunits that may facilitate their translocation across the plasma membranes into the inner cellular compartments. [50][51][52][61][62][63] This finding has stimulated a number of investigations on the design of synthetic aminoacid sequences, which self-assemble and enable the cellular internalization of various compounds.…”

“…[50][51][52][61][62][63] This finding has stimulated a number of investigations on the design of synthetic aminoacid sequences, which self-assemble and enable the cellular internalization of various compounds. [3][4][5][6][7][53][54][55][56][57][58][59][60] The large diversity of CPPs has been classified into sequences of cationic, anionic or neutral nature. 50 CPPs can be either protein-derived 53,73 or synthetic ones.…”

“…[50][51][52]75 CPPs may transport and deliver different types of bioactive molecules into living cells (anticancer drugs, RNA, DNA, or proteins). [3][4][5][6][7][35][36][37][38][39]54,[57][58][59][60] It is expected that CPPs derived from native 4 proteins and characterized by amphiphilic nature may be more efficient as drug delivery systems thanks to their self-assembly properties and low immunogenicity. When immerged in aqueous media, amphiphilic molecules (lipids, surfactants, peptides, lipid-drug or peptide-drug conjugates, etc.)…”

“…The focus of the present work is on bioinspired peptides with self-assembly properties as designed candidates for more efficient and safe drug delivery nanocarriers (Figure ). Cell-penetrating peptides (CPPs) are short sequences of amino acids (generally up to 35 aa), which have a capacity to cross the cellular bilayer membranes without damaging them. − The research on CPPs has been inspired by the fact that proteins (like transcription-activating factors, signal sequences, and homeoproteins) involve subunits that may facilitate their translocation across the plasma membranes into the inner cellular compartments. − ,− This finding has stimulated a number of investigations on the design of synthetic amino acid sequences, which self-assemble and enable the cellular internalization of various compounds. − ,− ,− The large diversity of CPPs has been classified into sequences of cationic, anionic, or neutral nature . CPPs can be either protein-derived , or synthetic ones. , Other CPP classifications regard their amphipathic character and their conformation type ( e.g .…”

“…CPPs can be either protein-derived , or synthetic ones. , Other CPP classifications regard their amphipathic character and their conformation type ( e.g . α-helical, β-sheet, or other). − , CPPs may transport and deliver different types of bioactive molecules into living cells (anticancer drugs, RNA, DNA, or proteins). − ,− ,,− It is expected that CPPs derived from native proteins and characterized by amphiphilic nature may be more efficient as drug delivery systems thanks to their self-assembly properties and low immunogenicity.…”