Peptide inhibitors of botulinum neurotoxin by mRNA display

Directing evolution of novel ligands by mRNA display

mRNA display is a powerful biological display platform for the directed evolution of proteins and peptides. mRNA display libraries covalently link the displayed peptide or protein (phenotype) with the encoding genetic information (genotype) through the biochemical activity of the small molecule puromycin. Selection for peptide/protein function is followed by amplification of the linked genetic material and generation of a library enriched in functional sequences. Iterative selection cycles are then performed until the desired level of function is achieved, at which time the identity of candidate peptides can be obtained by sequencing the genetic material. The purpose of this review is to discuss the development of mRNA display technology since its inception in 1997 and to comprehensively review its use in the selection of novel peptides and proteins. We begin with an overview of the biochemical mechanism of mRNA display and its variants with a particular focus on its advantages and disadvantages relative to other biological display technologies. We then discuss the importance of scaffold choice in mRNA display selections and review the results of selection experiments with biological (e.g., fibronectin) and linear peptide library architectures. We then explore recent progress in the development of "drug-like" peptides by mRNA display through the post-translational covalent macrocyclization and incorporation of non-proteogenic functionalities. We conclude with an examination of enabling technologies that increase the speed of selection experiments, enhance the information obtained in post-selection sequence analysis, and facilitate high-throughput characterization of lead compounds. We hope to provide the reader with a comprehensive view of current state and future trajectory of mRNA display and its broad utility as a peptide and protein design tool.

High-Throughput Screening Uncovers Novel Botulinum Neurotoxin Inhibitor Chemotypes

Botulism is caused by potent and specific bacterial neurotoxins that infect host neurons and block neurotransmitter release. Treatment for botulism is limited to administration of an antitoxin within a short time window, before the toxin enters neurons. Alternatively, current botulism drug development targets the toxin light chain, which is a zinc-dependent metalloprotease that is delivered into neurons and mediates long-term pathology. Several groups have identified inhibitory small molecules, peptides, or aptamers, although no molecule has advanced to the clinic due to a lack of efficacy in advanced models. Here we used a homogeneous high-throughput enzyme assay to screen three libraries of drug-like small molecules for new chemotypes that modulate recombinant botulinum neurotoxin light chain activity. High-throughput screening of 97088 compounds identified numerous small molecules that activate or inhibit metalloprotease activity. We describe four major classes of inhibitory compounds identified, detail their structure-activity relationships, and assess their relative inhibitory potency. A previously unreported chemotype in any context of enzyme inhibition is described with potent submicromolar inhibition (Ki = 200-300 nM). Additional detailed kinetic analyses and cellular cytotoxicity assays indicate the best compound from this series is a competitive inhibitor with cytotoxicity values around 4-5 μM. Given the potency and drug-like character of these lead compounds, further studies, including cellular activity assays and DMPK analysis, are justified.

Complementary DNA display selection of high-affinity peptides binding the vacuolating toxin (VacA) of Helicobacter pylori

Artificial peptides designed for molecular recognition of a bacterial toxin have been developed. Vacuolating cytotoxin A protein (VacA) is a major virulence factor of Helicobacter pylori, a gram-negative microaerophilic bacterium inhabiting the upper gastrointestinal tract, particularly the stomach. This study attempted to identify specific peptide sequences with high affinity for VacA using systematic directed evolution in vitro, a cDNA display method. A surface plasmon resonance-based biosensor and fluorescence correlation spectroscopy to examine binding of peptides with VacA identified a peptide (GRVNQRL) with high affinity. Cyclization of the peptide by attaching cysteine residues to both termini improved its binding affinity to VacA, with a dissociation constant (Kd ) of 58 nm. This study describes a new strategy for the development of artificial functional peptides, which are promising materials in biochemical analyses and medical applications.

Inhibition in vivo of the activity of botulinum neurotoxin A by small molecules selected by virtual screening

To search for small molecular size inhibitors of botulinum neurotoxin A (BoNT/A) endopeptidase activity, we have screened the NCI library containing about 1 million structures against the substrate binding pocket of BoNT/A. Virtual screening (VS) was performed with the software Glide (Grid-based ligand docking energetics) and the findings were confirmed by AutoDock. Ten compounds were found that had favorable energetic and glide criteria and 5 of these compounds were selected for their ability to protect mice in vivo against a lethal dose of BoNT/A. Each compound was incubated at different molar excesses with a lethal dose of the toxin and then the mixture injected intravenously into mice. At 4690 M excess, compounds NSC94520 and NSC99639 protected all (100%) the mice from lethal toxicity. Compounds NSC48461 and NSC627733 gave 75% protection. Compound NSC348884 showed the least inhibition of toxicity allowing only a fraction (25%) of the mice to survive challenge with a lethal dose; and in the case of the mice that did not survive there was a considerable delay of mortality. At 2400 M excess compounds NSC94520 remained fully protective while and NSC99639 afforded 75% protection and at 1200 M excess each of these two compounds gave 50% protection. The two compounds gave no protection at 600 or less molar excess. When each compound was administered intravenously at 4690 M excess at different times (from 1 h to 6 h) after the intravenous injection of the active toxin, none of the compounds was able to protect the animals from toxicity. The findings show the value of VS in identifying potential inhibitors of the toxin for further development and improvement.

The strange case of the botulinum neurotoxin: using chemistry and biology to modulate the most deadly poison

In the classic novella "The Strange Case of Dr. Jekyll and Mr. Hyde", Robert Louis Stevenson paints a stark picture of the duality of good and evil within a single man. Botulinum neurotoxin (BoNT), the most potent known toxin, possesses an analogous dichotomous nature: It shows a pronounced morbidity and mortality, but it is used with great effect in much lower doses in a wide range of clinical scenarios. Recently, tremendous strides have been made in the basic understanding of the structure and function of BoNT, which have translated into widespread efforts towards the discovery of biomacromolecules and small molecules that specifically modulate BoNT activity. Particular emphasis has been placed on the identification of inhibitors that can counteract BoNT exposure in the event of a bioterrorist attack. This Review summarizes the current advances in the development of therapeutics, including vaccines, peptides, and small-molecule inhibitors, for the prevention and treatment of botulism.

Molecular biology of botulinum neurotoxin serotype A: a cosmetic perspective

Cosmetic use of botulinum neurotoxin serotype A (BoNT/A) involves low doses of toxin administered for facial wrinkles and hyperhidrosis. The structural and functional properties of BoNT/A can affect the degree and duration of effect. Actively using the injected muscle is favorable as it exposes more receptors to BoNT/A. Divided doses of BoNT/A at an interval of more than 3 days may be longer lasting than single dose by blocking nascent neuronal sprouts. Antibodies are unlikely to be effective in BoNT/A neutralization because of the large area of receptor interaction. Several commonly used drugs including zinc and chloroquine can interact with BoNT/A, necessitating dosage adjustment for optimum effect. Serotype E (BoNT/E) can emerge as an antidote for BoNT/A for cosmetic use.

The use of small molecules to investigate molecular mechanisms and therapeutic targets for treatment of botulinum neurotoxin A intoxication

Botulinum neurotoxins (BoNTs) are agents responsible for botulism, a disease characterized by peripheral neuromuscular blockade and subsequent flaccid paralysis. The potent paralytic ability of these toxins has resulted in their use as a therapeutic; however, BoNTs are also classified by the Centers for Disease Control and Prevention as one of the six highest-risk threat agents of bioterrorism. Consequently, a thorough understanding of the molecular mechanism of BoNT toxicity is crucial before effective inhibitors and, ultimately, an approved drug can be developed. In this article, we systematically detail BoNT intoxication by examining each of the discrete steps in this process. Additionally, rationally designed strategies for combating the toxicity of the most potent BoNT serotype are evaluated.