Peptide-directed binding for the discovery of modulators of α-helix-mediated protein-protein interactions: Proof-of-concept studies with the apoptosis regulator Mcl-1

Targeting PPIs with small molecules can be challenging owing to large, hydrophobic binding surfaces. Herein, we describe a strategy that exploits selective α-helical PPIs, transferring these characteristics to small molecules. The proof of concept is demonstrated with the apoptosis regulator Mcl-1, commonly exploited by cancers to avoid cell death. Peptide-directed binding uses few synthetic transformations, requires the production of a small number of compounds, and generates a high percentage of hits. In this example, about 50 % of the small molecules prepared showed an IC50 value of less than 100 μm, and approximately 25 % had IC50 values below 1 μm to Mcl-1. Compounds show selectivity for Mcl-1 over other anti-apoptotic proteins, possess cytotoxicity to cancer cell lines, and induce hallmarks of apoptosis. This approach represents a novel and economic process for the rapid discovery of new α-helical PPI modulators

An α-Helix-Mimicking 12,13-Helix: Designed α/β/γ-Foldamers as Selective Inhibitors of Protein-Protein Interactions

A major current challenge in bioorganic chemistry is the identification of effective mimics of protein secondary structures that act as inhibitors of protein–protein interactions (PPIs). In this work, trans-2-aminocyclobutanecarboxylic acid (tACBC) was used as the key β-amino acid component in the design of α/β/γ-peptides to structurally mimic a native α-helix. Suitably functionalized α/β/γ-peptides assume an α-helix-mimicking 12,13-helix conformation in solution, exhibit enhanced proteolytic stability in comparison to the wild-type α-peptide parent sequence from which they are derived, and act as selective inhibitors of the p53/hDM2 interaction

Towards “Bionic” Proteins: Replacement of Continuous Sequences from HIF-1α with Proteomimetics to Create Functional p300 Binding HIF-1α Mimics

Using the HIF-1α transcription factor as a model, this manuscript illustrates how an extended sequence of α-amino acids in a polypeptide can be replaced with a non-natural topographical mimic of an α-helix comprised from an aromatic oligoamide. The resultant hybrid is capable of reproducing the molecular recognition profile of the p300 binding sequence of HIF-1α from which it is derived

Examination of the Effect of N‐terminal Diproline and Charged Side Chains on the Stabilization of Helical Conformation in Alanine–based Short Peptides: A Molecular Dynamics Study

The effect of N‐terminal diproline segment and charged side chains on the stabilization of helical conformation in alanine‐based short peptides are examined using molecular dynamics (MD) simulations. The cationic peptides, Ac–Pro1–Pro2–Ala3–Lys4–Ala5–Lys6–Ala7–Lys8–Ala9–NH2 (Ia) and Ac–DPro1–Pro2–Ala3–Lys4–Ala5–Lys6–Ala7–Lys8–Ala9–NH2 (IIa) are examined for the role of lysine side chains on the inducement of helical conformation in alanine‐based short peptides. To examine the influence of lysine and glutamic acid in the i, i + 4 arrangement on the stabilization of helical conformation, cationic peptides, Ia and IIa, are modified as ion‐pair peptides, Ac–Pro1–Pro2–Glu3–Glu4–Ala5–Ala6–Lys7–Lys8–Ala9–NH2 (Ib) and Ac–DPro1–Pro2–Glu3–Glu4–Ala5–Ala6–Lys7–Lys8–Ala9–NH2 (IIb), respectively. MD simulations manifest enhanced occupancies in the α basin of ϕ, ψ space for ion‐pair peptides as compare to cationic peptides. The radial distribution function (RDF) analysis highlight that large side chain substituents of lysine and glutamic acid assist in helix formation by blocking water molecules from solvating backbone CO and NH groups.N‐terminal diproline of homochiral structure, LPro–LPro, and large side chain substituents of lysine and glutamic acid residues in the i, i + 4 arrangement stabilize the helical conformation in alanine‐based nonapeptide, Ac–Pro1–Pro2–Glu3–Glu4–Ala5–Ala6–Lys7–Lys8–Ala9–NH2 (Ib), as observed in the second most‐populated microstate, m2, during molecular dynamics in explicit‐water.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/135318/1/slct201601381-sup-0001-misc_information.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/135318/2/slct201601381_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/135318/3/slct201601381.pd

Identification of β-strand mediated protein–protein interaction inhibitors using ligand-directed fragment ligation

β-Strand mediated protein–protein interactions (PPIs) represent underexploited targets for chemical probe development despite representing a significant proportion of known and therapeutically relevant PPI targets. β-Strand mimicry is challenging given that both amino acid side-chains and backbone hydrogen-bonds are typically required for molecular recognition, yet these are oriented along perpendicular vectors. This paper describes an alternative approach, using GKAP/SHANK1 PDZ as a model and dynamic ligation screening to identify small-molecule replacements for tranches of peptide sequence. A peptide truncation of GKAP functionalized at the N- and C-termini with acylhydrazone groups was used as an anchor. Reversible acylhydrazone bond exchange with a library of aldehyde fragments in the presence of the protein as template and in situ screening using a fluorescence anisotropy (FA) assay identified peptide hybrid hits with comparable affinity to the GKAP peptide binding sequence. Identified hits were validated using FA, ITC, NMR and X-ray crystallography to confirm selective inhibition of the target PDZ-mediated PPI and mode of binding. These analyses together with molecular dynamics simulations demonstrated the ligands make transient interactions with an unoccupied basic patch through electrostatic interactions, establishing proof-of-concept that this unbiased approach to ligand discovery represents a powerful addition to the armory of tools that can be used to identify PPI modulators

Synthesis, structural elucidation and biological evaluation of Pipecolidepsin A and Phakellistatin 19

[eng] Pipecolidepsin A is a cyclodepsipeptide produced by a Homophymia marine sponge that has shown interesting anticancer properties against several human cancer cell lines. From a structural point of view, it is a “head-to-side-chain” cyclodepsipeptide, in which the ester bond links the C-terminal and the side-chain of the unprecedented amino acid AHDMHA. This linkage provides a beta-branched arrangement that comprises a 25-membered macrolactone, and an exocyclic peptidic arm terminated with a polyketide moiety. Furthermore, Pipecolidepsin A contains up to 6 synthetic building blocks with several potential side reactions during the SPPS. The syntheses of the suitable protected derivatives of the amino acids L-threo-beta-EtO-Asn, AHDMHA and DADHOHA have been developed in our laboratory. Additionally, an already described procedure to synthesize the beta-hydroxyacid HTMHA was also adapted and reproduced. The biggest synthetic challenge of Pipecolidepsin A’s synthesis is the construction of the ester bond over an extremely hindered secondary alcohol. Thus, incorporation of the Alloc-pipecolic-OH moiety was studied at different growing stages of the peptide chain, meaning, after coupling of Fmoc-AHDMHA-OH, Fmoc-diMeGln-OH and Fmoc-DADHOHA(Acetonide, Trt)-OH residues. Moreover, when developing the synthetic scheme, some main potential side reactions and synthetic challenges were considered: consecutive coupling of extremely bulky residues, racemization, intramolecular lactamization of unprotected beta-amino diMe-Gln, aspartimides formation and dehydration to nitrile of the unprotected side-chain amides. A robust and reproducible synthetic strategy for Pipecolidepsin A has been developed for the first time. The chemical, structural and biological equivalence between natural and synthetic Pipecolidepsin A has been satisfactorily proved by means of HPLC-PDA co-elution, 1H and 13C NMR spectral assignment comparison, and biological evaluation of both compounds employing a colorimetric assay based on the sulforhodamine B reaction. Importantly, the synthetic scheme has been proved useful to provide straightforward access to analogs that will facilitate valuable structure-activity relationships (SARs). In addition, the synthesis of the cytotoxic proline-rich peptide Phakellistatin 19 was successfully achieved by using a combination of solid-phase and solution techniques. After chemical and spectral validation of the synthetic compound, biological evaluation revealed that synthetic Phakellistatin 19 did not display the same cytotoxicity of the natural counterpart. Thus, two different hypotheses were suggested and studied. The first one points out that preparations of natural Phakellistatins could contain a spectrally undetectable amount of a contamination (structurally related, eg. an epimer, or a totally different compound), which would be responsible for the biological activity. The second one argue that the presence of several Pro residues capable of cis-trans isomerism in a constrained macrocycle provides structures with a complex conformational profile. Individual conformers at Pro linkages bearing different biological properties could be stabilized in different conditions.[cat] Dos productes naturals marins de naturalesa peptídica han estat sintetitzats i estudiats estructuralment en la present tesi doctoral. El Pipecolidepsin A és un ciclodepsipèptid “cap-cadena lateral” que ha mostrat uns valors de citotoxicitat molt prometedors. Té una disposició estructural molt característica en la que un enllaç èster uneix l’extrem carboxil-terminal amb la cadena lateral de l’aminoàcid AHDMHA, originant d’aquesta manera una macrolactona de 25 membres i un braç peptídic exocíclic acabat amb un beta-hidroxiàcid. A més a més, la seva complexitat sintètica es veu incrementada per la presència en la seva estructura de fins a 6 aminoàcids sintètics no comercials. Les síntesis dels derivats correctament protegits dels residus L-threo-beta-EtO-Asn, AHDMHA, DADHOHA i HTMHA han estat desenvolupades i verificades al nostre laboratori. L’etapa crítica de la síntesi del Pipecolidepsin A és la formació de l’enllaç èster sobre un alcohol extremadament impedit. A més a més, són moltes les reaccions secundàries associades als diferents residus sintètics (deshidratació d’amides laterals a nitrils, racemització, formació d’aspartimides, lactamització intramolecular del residu DiMe-Gln quan l’amina està desprotegida...). Tot això es tindrà en compte durant el desenvolupament i validació de l’estratègia sintètica que donarà accés al Pipecolidepsin A, i obrirà la porta a la síntesi d’altres anàlegs i compostos relacionats. El Phakellistatin 19 és un pèptid cíclic homodètic ric en residus prolina. Un esquema sintètic que combina fase sòlida i solució ha estat satisfactòriament desenvolupat. No obstant i malgrat haver verificat l’equivalència química i espectral del Phakellistatin 19 sintètic, aquest no presenta el mateix comportament biològic que el natural. La possibilitat que una impuresa (en especial un epimer) espectralment no detectable sigui la responsable de la citotoxicitat, o bé que la presència de residus Pro capaços d’establir un equilibri cis-trans real generin un complex equilibri conformacional en el que els diferents confòrmers tinguin un perfil biològic diferent, han estat extensivament estudiades