Bisubstrate Inhibitors of Catechol O‐Methyltransferase (COMT): the Crucial Role of the Ribose Structural Unit for Inhibitor Binding Affinity

Abstract

Inhibition of the enzyme catechol O-methyltransferase offers a therapeutic handle to regulate the catabolism of catecholamine neurotransmitters, providing valuable assistance in the treatment of CNS disorders such as Parkinson's disease. A series of ribose-modified bisubstrate inhibitors of COMT featuring 2'-deoxy-, 3'-deoxy-, 2'-aminodeoxy-3'-deoxy-, and 2'-deoxy-3'-aminodeoxyribose-derived central moieties and analogues containing the carbocyclic skeleton of the natural product aristeromycin were synthesized and evaluated to investigate the molecular recognition properties of the ribose binding site in the enzyme. Key synthetic intermediates in the ribose-derived series were obtained by deoxygenative [1,2]-hydride shift rearrangement of adenosine derivatives; highlights in the synthesis of carbocyclic aristeromycin analogues include a diastereoselective cyclopropanation step and nucleobase introduction with a modified Mitsunobu protocol. In vitro biological evaluation and kinetic studies revealed dramatic effects of the ribose modification on binding affinity: 3'-deoxygenation of the ribose gave potent inhibitors (IC50 values in the nanomolar range), which stands in sharp contrast to the remarkable decrease in potency observed for 2'-deoxy derivatives (IC50 values in the micromolar range). Aminodeoxy analogues were only weakly active, whereas the change of the tetrahydrofuran skeleton to a carbocycle unexpectedly led to a complete loss of biological activity. These results confirm that the ribose structural unit of the bisubstrate inhibitors of COMT is a key element of molecular recognition and that modifications thereof are delicate and may lead to surprises.

Structure‐Based Design and Synthesis of the First Weak Non‐Phosphate Inhibitors for IspF, an Enzyme in the Non‐Mevalonate Pathway of Isoprenoid Biosynthesis

“…The latter was found to undergo ionic H-bonding with the OH residues of the ribose moieties in CMP [8b], CDP [8a], and analogues [6]. This contrasts our findings in the development of bisubstrate inhibitors of the enzyme catechol O-methyltransferase, which revealed a crucial role of the interaction between a ribose ring in the substrate and a glutamate side chain of the enzyme [16]. ii) Appropriate binding to the cytosine site in Pocket III by 2,5-diaminopyridines and derivatives of the nucleobase presumably yields the largest part of the measured driving force for complexation.…”

Molecular Recognition at the Active Site of Catechol‐O‐methyltransferase (COMT): Adenine Replacements in Bisubstrate Inhibitors

“…Synthesis: In contrast to earlier approaches, [14][15][16] in which adenine was introduced in the first step, the nucleobase substitutes in the new bisubstrate inhibitors 2 were introduced at a later stage of the synthesis (Scheme 1). [12,19] The general protocol involved amide coupling of allylic amine 3 with known activated catechol ester 4.…”

“…[12] The X-ray crystal structure of the ternary complex of ligand 1 (median inhibitory concentration IC 50 = 9 nm, inhibitory constant K i = 2 nm, [13] see Figure 1) with COMT and a Mg 2 + ion (PDB code: 1JR4) [14] was used as the basis for a detailed exploration of the molecular recognition properties of the entire active site of COMT. [15,16] Previously, we were able to demonstrate that 5-nitrocatechol anchors are not required for high-affinity bisubstrate inhibition and can be replaced with lipophilic substituents, such as a 4-fluorophenyl ring, without loss in activity against COMT. [17,18] The predicted orientation of the 4-fluorophenyl ring in the active site was recently confirmed by a series of X-ray cocrystal structure analyses.…”

Structure-based drug design of catechol-O-methyltransferase inhibitors for CNS disorders

“…The effects of ribose modification on ligand affinity were investigated [21,39]. Surprisingly, the minor change from the ribose ether oxygen atom to the CH2 unit of a carbocyclic cyclopentane core, in most cases, leads to complete loss of the binding affinity.…”

“…Surprisingly, the minor change from the ribose ether oxygen atom to the CH2 unit of a carbocyclic cyclopentane core, in most cases, leads to complete loss of the binding affinity. Although the exact reason is unknown, it was speculated that steric congestion in the ribose binding site (a narrow channel) that connects the adenine and catechol sites, as well as conformational changes upon replacement of the ribose moiety may play an important role [39]. The IC50 value of the 2′-deoxyribose derivative is increased by almost three orders of magnitude to 28 μM.…”