Synthesis, Characterization, and DNA Binding Profile of a Macrocyclic β-Sheet Analogue of ARC Protein

Abstract

ARC repressor (apoptosis repressor with caspase recruitment domain) is a protein which binds selectively to a specific sequence of DNA. In humans, ARC is primarily expressed in striated muscle tissue, which normally does not undergo rapid cell turnover. This suggests that ARC may play a protective role in the prevention against Duchenne Muscular Dystrophy and several types of tumors. In this Letter we report the synthesis, characterization, and conformational analysis of a β-sheet ARC repressor mimetic, based on the amino acid sequence of the β-sheet domain in the ARC protein. The ability of this β-sheet macrocycle to bind to double-stranded DNA was also evaluated using spectroscopic methods. Our data show that the synthetic peptide has a defined conformation and is able to bind DNA with reasonable affinity. These initial results lay the groundwork for the design of novel β-sheets folded peptides as valuable substitutes of transcription factor proteins in drug therapy.

New Teixobactin Analogues with a Total Lactam Ring

“…The standard SPPS procedure was followed, using 3 equiv of each amino acid for each coupling and HBTU (3 equiv), HOBt (3 equiv), and DIPEA (6 equiv) dissolved in 4 mL of DMF as the coupling mixture. , 120 mg of 2-CT-Cl resin (1 equiv) was weighed into a syringe for manual solid phase synthesis and swelled in DCM (8 mL) for 1 h with an automatic shaker. For the first coupling, 5 mL of a DCM solution containing the first amino acid and DIPEA was added to the resin and shaken overnight.…”

“…Furthermore, teixobactin interacts as β-sheet dimer with cell wall membrane components, thus generating two cavities comprising the C -terminal cycle and N -terminus acting as receptor for pyrophosphate groups via hydrogen bonding . As observed by the X-ray crystallographic structure of teixobactin analogues, a lactam bridge in place of a lactone may improve the interaction with lipids II and III; however, ring expansion resulted in analogues with very poor activity. , The solid state NMR work reported by Shukla and co-workers helps to clarify the importance of the relative stereochemistry and structural features of teixobactin: The use of a labeled analogue reveals the ability of this molecule to form a large cluster on the membrane surface by oligomerization of lipid II-binding teixobactin. − This molecule assumes a β-sheet form in which the critical sequence of d - and l -amino acids allows separation of hydrophobic and hydrophilic side chains located at the same side of the β-sheet, a common behavior of diverse naturally occurring peptides. − The peptide head containing ring interacts with N -acetyl muramic acid and to a minor extent with N -acetyl-glucosamine; the tail is anchored on the membrane surface by two isoleucines. In this way teixobactin significantly perturbs the bacterial membrane lipids and cell wall biosynthesis. , …”

Orthogonal threading‐through‐β‐sheet design of lung cancer EGFR extracellular domain‐derived peptidic mimotopes binding to anti‐EGFR antibody

“…All these works, however, have been done by creating and screening against a random combinatorial peptide library, and therefore, the obtained peptidic mimotopes are generally weak and exhibit broad specificity. Recently, Stefanucci et al (2015Stefanucci et al ( , 2021 demonstrated that the linear and cyclic βhairpin peptides can be rationally derived from the intermolecular interaction interface between ARC repressor and DNA, which exhibit a potential binding property to the cognate site of DNA major groove.…”

On resin click-chemistry-mediated synthesis of novel enkephalin analogues with potent anti-nociceptive activity

“…12 . Cyclic peptidomimetics are usually characterized by: ( i ) folding in a rigid structure 13 ; ( ii ) an improved metabolic stability compared to the linear counterparts 14 ; ( iii ) better penetration of the blood-brain barrier (BBB) 15 ; ( iv ) improved oral bioavailability and rapid excretion 16 ; ( v ) and a better pharmacological profile in terms of potency and selectivity 17 . These features could make DPDPE and other analogues good candidates as leads for drug development, as peptides are generally characterized by high selectivity and low toxicity 18 .…”