The Precise Chemical–Physical Nature of the Pharmacore in FK506 Binding Protein Inhibition: ElteX, a New Class of Nanomolar FKBP12 Ligands

Abstract

Due to its central role in immunosuppression and cell proliferation and due to its specific peptidyl-prolyl-isomerase (PPI) function, the FKBP protein family is at the crossroad of several important metabolic pathways. Members of this family, and notably FK506 binding protein (FKBP12), are thought to be involved in neurodegenerative diseases such as Alzheimer disease, Parkinson disease, multiple sclerosis, amyotrophic lateral sclerosis, as well as in proliferation disorders and cancer. Using an interdisciplinary approach based on computational, synthetic, and experimental techniques, we show that the best potential binders for FKBP proteins optimally expose the two contiguous carbonyl oxygen in the proline-mimetic chain for FKBP docking and are characterized by the abundance of rigid quasi-cyclic structures stabilized in aqueous solution by intraligand hydrophobic interactions mimicking the macrolide structure of the natural FKBP binders FK506 and Rapamycin. These peculiar structural and chemical-physical features define at the same time an ElteX compound and the minimal pharmacore in the FKBP family, shedding new light on the isomerization mechanism of the PPI domain. On the basis of the above hypothesis, we have successfully designed and synthesized several nanomolar ElteX FKBP12 ligands. Among these, ElteN378 is a new low atomic weight ligand with affinity comparable to that of the macrolide Rapamycin.

Electronic circular dichroism and nuclear magnetic resonance studies of peptides derived from the FKBP52‐interacting β‐turn of the hERα ligand‐binding domain

“…This “favored” orientation in fact corresponds to the distance between the carbonyl oxygens on either side of the prolyl/pipecolyl moiety (e.g., FK506/Elten 378). In the context of the Elten series of molecules, which represent an apparent “minimum” motif for FKBP12 binding, the preferred conformer has an almost ideal dicarbonyl orientation for H‐bonding with conserved amino acids . In the context of a peptide, this translates to the formation of an obligatory cis Xaa‐Pro bond and hence to a type VIa or type VIb turn as observed directly in the crystal structure complex of peptides with the FKBP protein SlyD …”

“…The interaction of FKBP52 with the hERα‐LBD may occur through its FK1 domain. The majority of synthetic FKBP FK1 ligands that are inspired from the immunomodulatory macrolides of highest affinity for this domain such as rapamycin or tacrolimus (FK506), typically exhibit (a) a spatial turn‐like orientation, as shown with cyclic or quasi cyclic immunomodulators, (b) a hydrophobic structure, and (c) an appropriate orientation of electron acceptor chemical groups (e.g., α‐keto amide motif or sulfonamide) prone to hydrogen bonding with specific residues forming the binding site . This “favored” orientation in fact corresponds to the distance between the carbonyl oxygens on either side of the prolyl/pipecolyl moiety (e.g., FK506/Elten 378).…”

Nanolayers for early diagnostics of proteins involved in degenerative amyloidosis

“…An efficient fluorescence quenching of FKBP12 was observed upon addition of the ligands in solution. The dissociation constants, K d , for FK506 and Rfx were calculated according to literature and recent studies in our group [7,8] The ligands were embedded in a planar scaffold using a biomimetic approach: that is to say preparing Langmuir-Blodgett films of phospholipids. The optimal phospholipid composition for each ligand has been established from the analysis of previous literature [9] combined with our own experimental work.…”

“…These results pave the way to important applications of these nanostructures, to name a few phospholipid formulation of liposomal systems for drug delivery as well as sensitive and specific nanosensors for FKBP12 for the early diagnosis of neurodegenerative amyloidosis. Studies of functionalized synthetic ligands [7] with surface-anchors and suitable spacers are currently in progress for the preparation of chemically modified surfaces [13] that can be directly coupled to sensing device for FKBP12.…”

I. Dissociation free energies of drug–receptor systems via non-equilibrium alchemical simulations: a theoretical framework

“…The ligand, by filling the exclusion zone of the receptor, inhibits its conformational motion and that of the protein residues delimiting the binding site, hence reducing the conformational entropy of the complex. Once the N τ NE independent trajectories from these states are [66]. N-Elte378, a conformationally dis-ordered molecule, can be characterized in water by a competition between extended and compact conformations (see Figure 7 of ref.…”