Substrate-selective inhibition of monoamine oxidase by some cyclopropylamino substituted oxadiazoles

Computational design of substrate selective inhibition

Most enzymes act on more than a single substrate. There is frequently a need to block the production of a single pathogenic outcome of enzymatic activity on a substrate but to avoid blocking others of its catalytic actions. Full blocking might cause severe side effects because some products of that catalysis may be vital. Substrate selectivity is required but not possible to achieve by blocking the catalytic residues of an enzyme. That is the basis of the need for "Substrate Selective Inhibitors" (SSI), and there are several molecules characterized as SSI. However, none have yet been designed or discovered by computational methods. We demonstrate a computational approach to the discovery of Substrate Selective Inhibitors for one enzyme, Prolyl Oligopeptidase (POP) (E.C 3.4.21.26), a serine protease which cleaves small peptides between Pro and other amino acids. Among those are Thyrotropin Releasing Hormone (TRH) and Angiotensin-III (Ang-III), differing in both their binding (K_m) and in turnover (k_cat). We used our in-house "Iterative Stochastic Elimination" (ISE) algorithm and the structure-based "Pharmacophore" approach to construct two models for identifying SSI of POP. A dataset of ~1.8 million commercially available molecules was initially reduced to less than 12,000 which were screened by these models to a final set of 20 molecules which were sent for experimental validation (five random molecules were tested for comparison). Two molecules out of these 20, one with a high score in the ISE model, the other successful in the pharmacophore model, were confirmed by in vitro measurements. One is a competitive inhibitor of Ang-III (increases its K_m), but non-competitive towards TRH (decreases its V_max).

Many proteins are enzymes—"catalytic machines" performing chemical reactions on "substrates"–which may be small or large molecules. Evolution optimized the speed of enzyme reactions, but mutations or excessive enzyme production could lead to non-controlled, accelerated activity, which must be blocked to avoid a product that promotes disease. Many inhibitors of enzymatic activity became drugs which can block the production of the aberrant product, due to blocking the enzymatic "machinery", the amino acids involved in catalysis. Most enzymes have several substrates and so, those other substrates are blocked too. Those may be vital to the well-being of cells and life and total inhibition is prone to cause serious side effects. It is therefore essential to solve the need for inhibition of a single substrate without inhibiting others. We have thus developed computational methods to block specifically the "culprit" substrate while allowing the enzyme machine to act on other substrates. By applying these computational methods, we predicted candidates for inhibiting one out of two substrates ("substrate selective inhibition") of a well-known enzyme reaction. In collaboration with a research group that excels in studying that specific enzyme (prolyl oligopeptidase) we found that two candidates out of a set of twenty that we picked out of 1.8 million molecules by filtering through computer models—are indeed selective to one substrate vis-a-vis the other (five random molecules were tested for comparison). This may be the first example of a computational method leading to substrate selective inhibitor drugs which could avoid side effects.

90 years of monoamine oxidase: some progress and some confusion

It would not be practical to attempt to deal with all the advances that have informed our understanding of the behavior and functions of this enzyme over the past 90 years. This account concentrates key advances that explain why the monoamine oxidases remain of pharmacological and biochemical interest and on some areas of continuing uncertainty. Some issues that remain to be understood or are in need of further clarification are highlighted.

The potential use of mechanism-based enzyme inactivators in medicine

Mechanism-based enzyme inactivator, alanine racemase, S-adenosylhomocysteine hydrolase, D-amino acid aminotransferase, gamma-aminobutyric acid aminotransferase, arginine decarboxylase, aromatase, L-aromatic amino acid decarboxylase, dihydrofolate reductase, dihydroorotate dehydrogenase DNA polymerase I, dopamine beta-hydroxylase, histidine decarboxylase, beta-lactamase, monoamine oxidase, ornithine decarboxylase, serine proteases, testosterone 5 alpha-reductase, thymidylate synthetase, xanthine oxidase.

Studies on the metabolism of dimethylnitrosamine in vitro by rat-liver preparations. II. Inhibition by substrates and inhibitors of monoamine oxidase

1. The metabolism of dimethylnitrosamine (DMN) to formaldehyde by rat-hepatic postmitochondrial supernatant fractions has been compared with the activities of several cytochrome P-450-dependent mixed-function oxidase enzymes and the Ziegler mixed-function amine oxidase enzyme (EC 1.14.13.8). 2. A variety of monoamine oxidase (MAO, EC 1.4.3.4) inhibitors of diverse chemical structure inhibited the metabolism of DMN. In parallel studies a number of MAO substrates, but not their deaminated products, also inhibited DMN metabolism, whereas substrates of diamine oxidase were ineffective. 3. At concentrations which inhibited DMN metabolism several MAO substrates and inhibitors did not inhibit the N-oxidation of N, N-dimethylaniline and an inhibitor and an activator of the Ziegler enzyme had no corresponding effect on DMN metabolism. 4. The metabolism of DMN and a number of MAO enzyme activities were stable to storage under conditions where mixed-function oxidase enzymes were not. 5. These results are consistent with the suggestion that DMN may, at least in part, be metabolized by hepatic enzyme(s) not dependent on cytochrome P-450 and that a microsomal amine oxidase enzyme, unrelated to the Ziegler enzyme, may be involved in the hepatic degradation of this nitrosamine. The present data does, however, suggest a role for microsomal NADPH-cytochrome c reductase in hepatic DMN metabolism.

Inhibition of rabbit liver monoamine oxidase by nitro aromatic compounds

Nitrobenzoid, nitroheterocyclic and cyanobenzoid compounds inhibit type B monoamine oxidase. A partially purified enzyme preparation from rabbit liver mitochondria, oxidizing rho-dimethyl-aminobenzylamine as the substrate, was competitively inhibited by nitrobenzoid compounds with K1 values in the range of 0.28 muM for rho-dinitrobenzene to 0.56 muM for rho-nitrobenzoic acid. The potencies of nitrobenzoid compounds were positively correlated with the Hammett sigma value for each substituent on nitrobenzene. Dinitro derivatives were slightly more potent than the corresponding mononitro compounds but not as potent as would be expected from their sigma values. For the nitroheterocyclic compounds, inhibition was also competitive; the lowest K1 was 1.3 muM for 5-nitrofurfural semicarbazone (nitrofurazone). Compounds with cyano groups in place of nitro groups were also inhibitory; the most potent was rho-acetobenzonitrile with a K1 of 1.3 muM. The results of this study indicate that, in addition to nitrobenzoid compounds, other compounds with planar, electron-deficient nuclei are effective inhibitors of type B monoamine oxidase. Although hydrophobic and steric parameters may play some role in inhibition, the predominant factor is the electron-withdrawing power of the ring substituents.