Effect of molecular clips and tweezers on enzymatic reactions by binding coenzymes and basic amino acids

Abstract

The tetramethylene-bridged molecular tweezers bearing lithium methanephosphonate or dilithium phosphate substituents in the central benzene or naphthalene spacer-unit and the dimethylene-bridged clips containing naphthalene or anthracene sidewalls substituted by lithium methanephosphonate, dilithium phosphate, or sodium sulfate groups in the central benzene spacer-unit are water-soluble. The molecular clips having planar naphthalene sidewalls bind flat aromatic guest molecules preferentially, for example, the nicotinamide ring and/or the adenine-unit in the nucleotides NAD(P) + , NMN, or AMP, whereas the benzene-spaced molecular tweezers with their bent sidewalls form stable host-guest complexes with the aliphatic side chains of basic amino acids such as lysine and argenine. The phosphonate-substituted tweezer and the clips having an extended central naphthalene spacer-unit or extended anthracene and benzo[k]fluoranthene sidewalls, respectively, form highly stable self-assembled dimers in aqueous solution, evidently due to non-classical hydrophobic interactions. The phosphate-substituted molecular clip containing naphthalene sidewalls inhibits the enzymatic, ADH-catalyzed ethanol oxidation by binding the cofactor NAD + in a competitive reaction. Surprisingly, tweezer-bearing phosphate substituents in the central benzene spacer-unit are more efficient inhibitors for the ethanol oxidation than the correspondingly substituted naphthalene clip, even though the tweezer does not bind the cofactor NAD + within the limits of detection. The phosphate-substituted naphthalene clip is, however, a highly efficient inhibitor of the enzymatic oxidation of glucose-6-phosphate (G6P) with NADP + catalyzed by glucose-6-phosphate dehydrogenase (G6PD), whereas the phosphonate-substituted clip only functions as an inhibitor by forming a complex with the cofactor. Detailed kinetic, thermodynamic, and computational modeling studies provide insight into the mechanism of these novel enzyme inhibition reactions.

A molecular tweezer antagonizes seminal amyloids and HIV infection

“…We found that CLR01, but not CLR03, neutralized the positive surface charge of SEVI, PAP85-120, and SEM1(49-107) fibrils within minutes ( Figure 4A ). Notably, pre-treatment of CLR01 with lysine or poly-L-lysine abrogated the fibril neutralizing activity of CLR01 ( Figure 4—figure supplement 1 ), which further supports previous findings concerning the specificity underlying these interactions ( Fokkens et al, 2005 ; Klärner et al, 2006 , 2010 ). Next, confocal microscopy was used to assess whether this neutralization could abrogate fibril binding to YFP-tagged virions.…”

“…The lysine- and arginine-specific molecular tweezer, CLR01 ( Figure 1A,B ) ( Fokkens et al, 2005 ; Klärner et al, 2006 , 2010 ), inhibits amyloid fibrillization by engaging specific lysine, arginine, or both residues within a variety of disease-associated amyloidogenic proteins including amyloid-β protein (Aβ), tau, islet amyloid polypeptide, transthyretin, and α-synuclein ( Sinha et al, 2011 ; Attar et al, 2012 ; Prabhudesai et al, 2012 ; Sinha et al, 2012 ; Acharya et al, 2014 ; Ferreira et al, 2014 ; Lopes et al, 2015 ; Zheng et al, 2015 ). Furthermore, CLR01 has even been found to slowly remodel preformed Aβ and α-synuclein fibrils over the course of several weeks ( Sinha et al, 2011 ; Prabhudesai et al, 2012 ).…”

“…Indeed, it is important to note that the specificity of CLR01 binding to lysine or arginine is well established. CLR01 was tested against almost all naturally occurring amino acid residues in model compounds, and does not bind to any other amino acid side chain except for lysine ( K d ∼10 µM) and arginine ( K d ∼50 µM) ( Fokkens et al, 2005 ; Klärner et al, 2006 ; Klärner et al, 2010 ). The structure of the CLR01-lysine complex and the precise mechanism of lysine threading into the CLR01 guest cavity and subsequent ion pairing have been extensively characterized by NMR spectroscopy, crystal structure, molecular dynamics, and quantum mechanics/molecular mechanics (QM/MM) calculations ( Bier et al, 2013 ; Dutt et al, 2013 ; Klärner and Schrader, 2013 ).…”

Linker Effects on Amino Acid and Peptide Recognition by Molecular Tweezers

“…Crown ethers and cryptands, calixarenes and cucurbiturils all benefit from this design, albeit with the disadvantage that it favors cyclic or symmetric guests. [4][5][6][7][8][9][10][11][12][13] These draw the biologically active part of the respective cofactor (NAD + or NADP + ) [5,6,9] or amino acid (the side chain of Lys and Arg) [5][6][7][8][9][10][11][12][13][14] into their cavities, which enables them to reversibly inhibit enzymatic processes as well as protein aggregation events. [1][2][3] Among other things, the introduction of new side arms that can be accommodated within the interior of the macrocycle must be strictly avoided, because this severely impedes guest inclusion.…”

Cooperative heterodimer formation between per-guadinylated and carboxylated or phosphorylated cyclodextrins in DMSO and DMSO–water studied by NMR spectroscopy and microcalorimetry

“…The new entities will posses a well-defined structure in solution and be capable of binding other molecules. Thus a vast array of functional supramolecular architectures (capsules, tweezers, clips, e.t.c) has be created (1,2,3,4,5,6).…”