Biologically Active Peptides from Venoms: Applications in Antibiotic Resistance, Cancer, and Beyond

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Peptides are potential therapeutic alternatives against global diseases, such as antimicrobial-resistant infections and cancer. Venoms are a rich source of bioactive peptides that have evolved over time to act on specific targets of the prey. Peptides are one of the main components responsible for the biological activity and toxicity of venoms. South American organisms such as scorpions, snakes, and spiders are important producers of a myriad of peptides with different biological activities. In this review, we report the main venom-derived peptide families produced from South American organisms and their corresponding activities and biological targets.

From 2015 to 2020 the U.S. Food Drug Administration (FDA) approved 273 new drugs. Out of those, 21 were peptides or peptide-derived drugs described as medicines or drug delivery systems. The sales of peptide drugs exceeded US$ 70 billion in 2019 with 10 non-insulin peptide drugs in the top 200 drug sales, representing a substantial part of the pharmaceutical market.

DNA Ligase-Mediated Translation of DNA Into Densely Functionalized Nucleic Acid Polymers

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We developed a method to translate DNA sequences into densely functionalized nucleic acids by using T4 DNA ligase to mediate the DNA-templated polymerization of 5′-phosphorylated trinucleotides containing a wide variety of appended functional groups. This polymerization proceeds sequence specifically along a DNA template and can generate polymers of at least 50 building blocks (150 nucleotides) in length with remarkable efficiency. The resulting single-stranded highly modified nucleic acid is a suitable template for primer extension using deep vent (exo-) DNA polymerase, thereby enabling the regeneration of template DNA. We integrated these capabilities to perform iterated cycles of in vitro translation, selection, and template regeneration on libraries of modified nucleic acid polymers.

Inspired by the trinucleotide coding system used during ribosomal translation of mRNA into proteins, we chose 5′-phosphorylated trinucleotides as the functionalized monomers to be polymerized by T4 DNA ligase. Such a system would enable up to 64 different modifications to be incorporated sequence specifically throughout a nucleic acid polymer. Although the shortest T4 DNA ligase substrate previously reported was a pentamer, we hypothesized that optimization of ligation conditions might enable the polymerization of modified trinucleotides. Because T4 DNA ligase is known to be inefficient at ligating substrates separated by a gap when hybridized to a template, we envisaged the translation process occurring within a reading frame defined by a 5′-phosphorylated initiation primer and a nonphosphorylated termination primer.

In summary, we have developed a new system for the translation of DNA templates into sequence-defined highly functionalized nucleic acid polymers that uses T4 DNA ligase to catalyze the DNA-templated polymerization of functionalized trinucleotides. We incorporated eight different functional groups throughout a polymer product, with the possibility of expanding the substrate set up to 64. In addition to exhibiting a high degree of sequence specificity, polymerization was remarkably efficient and could generate a polymer of 50 consecutive substrates (150 nucleotides), corresponding to a polymer of a molecular weight of approximately 60 kDa. The functionalized nucleic acid polymers were amenable to primer extension by deep vent (exo-) to regenerate the encoding template with high fidelity. Iterative cycles of translation, selection, template regeneration, and PCR amplification enabled the enrichment of a single library member encoding a carbonic anhydrase II inhibitor from a library of 5.8 × 106 highly functionalized DNAs. The ability to sequence specifically introduce a wide array of functionality within an evolvable nucleic acid polymer should increase their structural and functional capabilities and therefore may help bridge the gap between nucleic acid polymers and proteins.(J Am Chem Soc. 2013 Jan 9; 135(1): 98–101.)

Therapeutic phosphorodiamidate morpholino oligonucleotides: Physical properties, solution structures, and folding thermodynamics

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Elucidating the structure-function relationships for therapeutic RNA mimicking phosphorodiamidate morpholino oligonucleotides (PMOs) is challenging due to the lack of information about their structures. While PMOs have been approved by the US Food and Drug Administration for treatment of Duchenne muscular dystrophy, no structural information on these unique, charge-neutral, and stable molecules is available. We performed circular dichroism and solution viscosity measurements combined with molecular dynamics simulations and machine learning to resolve solution structures of 22-mer, 25-mer, and 30-mer length PMOs. The PMO conformational dynamics are defined by the competition between non-polar nucleobases and uncharged phosphorodiamidate groups for shielding from solvent exposure. PMO molecules form non-canonical, partially helical, stable folded structures with a small 1.4- to 1.7-nm radius of gyration, low count of three to six base pairs and six to nine base stacks, characterized by −34 to −51 kcal/mol free energy, −57 to −103 kcal/mol enthalpy, and −23 to −53 kcal/mol entropy for folding. The 4.5- to 6.2-cm3/g intrinsic viscosity and Huggins constant of 4.5–9.9 are indicative of extended and aggregating systems. The results obtained highlight the importance of the conformational ensemble view of PMO solution structures, thermodynamic stability of their non-canonical structures, and concentration-dependent viscosity properties. These principles form a paradigm to understand the structure-properties-function relationship for therapeutic PMOs to advance the design of new RNA-mimic-based drugs.

Phosphorodiamidate morpholino oligonucleotides (PMOs) ) are a subclass of antisense oligonucleotides (ASOs) that have the canonical nucleic acid backbone replaced by morpholino rings connected by phosphorodiamidate linkages.They are single-stranded DNA analogs that have favorable biophysical properties, including high solubility in an aqueous medium, low to no metabolic degradation primarily due to their neutral charge, and high duplex stability, which make this class of compounds useful as potential therapeutics. PMOs have been approved by the US Food and Drug Administration (FDA) for the treatment of Duchenne muscular dystrophy (DMD) since 2016, and they have been designed to target Marburg, Ebola,Picornaviruses, and other viruses,along with bacterial targets and have been developed as anti-cancer agents. For treatment of DMD, PMOs can be designed to target regions of the dystrophin pre-mRNA to allow skipping of a targeted exon, and restoration of the mRNA reading frame allowing for translation of a shortened, yet functional, dystrophin protein. PMOs can be designed to bind to complementary sequences in target mRNA by Watson-Crick base pairing to effectively block translation through an RNase H-independent steric blockade.Furthermore, PMOs can also be effective as antiviral agents, since the formation of a PMO:mRNA duplex may effectively block translation of the viral RNA genome, thereby inhibiting viral replication.PMOs have been shown to resist the activity of a variety of enzymes present in biological fluids, including nucleases, proteases, esterases, and hydrolases.In addition, due to their uncharged backbone and overall neutral charge, interactions of PMO with cellular proteins are minimal, helping to limit therapeutic side effects.(