Computational Design of Macrocyclic Binders of S100B(ββ): Novel Peptide Theranostics

Srinivasaraghavan Kannan,Chandra S. Verma,Jianguo Li,Pietro G. A. Aronica,Thanh Binh Nguyen

doi:10.3390/molecules26030721

Abstract

S100B(ββ) proteins are a family of multifunctional proteins that are present in several tissues and regulate a wide variety of cellular processes. Their altered expression levels have been associated with several human diseases, such as cancer, inflammatory disorders and neurodegenerative conditions, and hence are of interest as a therapeutic target and a biomarker. Small molecule inhibitors of S100B(ββ) have achieved limited success. Guided by the wealth of available experimental structures of S100B(ββ) in complex with diverse peptides from various protein interacting partners, we combine comparative structural analysis and molecular dynamics simulations to design a series of peptides and their analogues (stapled) as S100B(ββ) binders. The stapled peptides were subject to in silico mutagenesis experiments, resulting in optimized analogues that are predicted to bind to S100B(ββ) with high affinity, and were also modified with imaging agents to serve as diagnostic tools. These stapled peptides can serve as theranostics, which can be used to not only diagnose the levels of S100B(ββ) but also to disrupt the interactions of S100B(ββ) with partner proteins which drive disease progression, thus serving as novel therapeutics.

Highlights

S100B(ββ) is among the most extensively studied members of a highly conserved group of Ca2+ -binding proteins engaged in multiple protein–protein interactions (PPI) [1,2,3,4,5].Its functional unit is a dimer which can be disulfide-linked at the dimer interface or exist as a noncovalent dimer under reducing conditions
Molecular Dynamics (MD) simulations were carried out to understand the dynamics of the S100B(ββ)peptide complexes
During the molecular dynamics (MD) simulations, the S100B(ββ)-peptide complexes remained stable with no unbinding of peptides observed

Summary

Introduction

S100B(ββ) is among the most extensively studied members of a highly conserved group of Ca2+ -binding proteins engaged in multiple protein–protein interactions (PPI) [1,2,3,4,5].Its functional unit is a dimer (homo or hetero) which can be disulfide-linked at the dimer interface or exist as a noncovalent dimer under reducing conditions. In the reduced form, the two subunits of S100B(ββ) associate tightly (Kd < 500 pM) into a compact dimer which is characterized by a highly charged surface and an extensive hydrophobic interface [6,7,8,9,10,11,12,13,14]. The first helix–loop–helix motif connecting h1, loop, h2 is referred to as a pseudo-EF-hand, whereas the second helix–loop–helix motif connecting h3, loop, h4 makes up the canonical EF-hand These two motifs are connected by a “hinge” region, which consists of 10–12 residues and is very important for target interactions. Intracellular S100B(ββ) plays a role in the regulation the canonical EF-hand Binding of Ca2+ results in a large conformational change in S100B, with h3 oriented perpendicular to h4, exposing a hydrophobic cleft made up of residues from h2, h3 and h4, and is the region where

Methods

Results

Conclusion