Molecular basis of cyclooxygenase enzymes (COXs) selective inhibition

Abstract

The widely used nonsteroidal anti-inflammatory drugs block the cyclooxygenase enzymes (COXs) and are clinically used for the treatment of inflammation, pain, and cancers. A selective inhibition of the different isoforms, particularly COX-2, is desirable, and consequently a deeper understanding of the molecular basis of selective inhibition is of great demand. Using an advanced computational technique we have simulated the full dissociation process of a highly potent and selective inhibitor, SC-558, in both COX-1 and COX-2. We have found a previously unreported alternative binding mode in COX-2 explaining the time-dependent inhibition exhibited by this class of inhibitors and consequently their long residence time inside this isoform. Our metadynamics-based approach allows us to illuminate the highly dynamical character of the ligand/protein recognition process, thus explaining a wealth of experimental data and paving the way to an innovative strategy for designing new COX inhibitors with tuned selectivity.nonsteroidal anti-inflammatory drugs | COX selectivity | coxibs | path collective variables | metadynamics N onsteroidal anti-inflammatory drugs (NSAIDs) are widely used as therapeutic agents for the treatment of pain and inflammation, and in addition several evidences have been very recently reported on their chemopreventive effect in colorectal cancer (1). Their mechanism of action is based on the blockage of the cyclooxygenase enzymes (COXs) (2) by sterically hindering the entrance of the physiological binder arachidonic acid. The classical NSAIDs such as aspirin, ibuprofen, or flurbiprofen are nonselective and inhibit indifferently all the COXs isoforms. In the last few decades, the interest of scientists has been mostly focused on a selective inhibition between COX-1/COX-2. In fact, the inhibition of COX-1, particularly in the gastrointestinal system, may lead to dangerous side effects such as ulcers. As a consequence, a selective inhibition of COX-2 has been sought for decades, and recently a new generation of NSAIDs, namely coxibs, was found. However, some of them, such as rofecoxib (Vioxx®), have been withdrawn from the market due to their cardiotoxicity (3-5). This was not the case of other COX-2 selective drugs such as celecoxib and nimesulide, with the latter one largely used as an anti-inflammatory agent in many diseases. As a consequence, today, in the rational design of new COXs binders, medicinal chemists have to pay attention to the selectivity properties of the designed drugs, and a fine-tuning of the COX selectivity profile might be necessary to generate novel effective drugs with reduced side effects. In the rational modulation of the binders selectivity precious help comes from the x-ray crystallography. In fact, the crystallographic structures show that selective and nonselective inhibitors generally bind in two different patterns. In COX-1, the space of the selectivity pocket is reduced due to the presence of Ile523, while in COX-2 the presence of Val523 augments the available space provid...

Molecular Basis of Binding Interactions of NSAIDs and Computer-Aided Drug Design Approaches in the Pursuit of the Development of Cyclooxygenase-2 (COX-2) Selective Inhibitors

“…The triluoromethyl group atached to the pyrazole ring is surrounded by a close hydrophobic cavity formed by Met113, Val116, Val349, Tyr355, Leu359 and Leu531 where only Arg120 (located near to CF 3 group) introduces a strong electrostatic ield. This cavity is referred to as common pocket ( Figure 4A) as it is also found to be occupied by the aromatic ring bearing the carboxylate functional group of many nonselective COX inhibitors such as ibuprofen and lurbiprofen, respectively [38]. Furthermore, these two features of SC-558 binding are almost equivalent to the binding mode of lurbiprofen and indomethacin [33].…”

“…Vitorio et al used an advanced metadynamics-based computational technique to simulate the full dissociation process of a highly potent and selective inhibitor SC-558 in both COX-1 and COX-2 isoenzymes [38]. The metadynamics study of SC-558 dissociation process in COX-2 was able to reproduce the X-ray crystallographic pose and also revealed the possibility of an alternative binding mode (Figure 6A and B).…”

“…The experimentally observed time-dependent slow tight-binding inhibition of other diaryl heterocyclic compounds similar to SC-558 is interpreted due to the presence of an additional binding step, where a vital role might be played by the rearrangement of the hydrogen-bonding network formed by Arg120, Tyr355 and Glu524, respectively, which are assumed to be critical for the transition from the relaxed to the tightened state of the enzyme. The involvement of these key residues (Arg120 and Tyr355) in the newly observed alternative binding mode of SC-558 suggests that the time-dependent inhibition kinetics of SC-558 results from the ability of the ligand to bind in two distinct but equally strong ways [38].…”

“…The phenylsulphonamide moiety of SC-558 is found to be anchored within a selectivity pocket formed by His90, Asn192, Leu352, Ser353, Arg513, Ala516, Ile517, Phe518 and Val523 assuming a conformation in which one of the oxygen atoms forms H-bond with Arg513 and is close enough to interact with His90, while the amide hydrogens are able to interact with the backbone of Phe518 through two water bridges. The phenylsulphonamide moiety of SC-558 is mainly responsible for inducing selectivity for COX-2, where it is easily accessible to the selectivity pocket due to the presence of smaller residue Val523 that is more restricted in COX-1 because of the substitution of valine to isoleucine at the same position-523 [33,38].…”

Bases moleculares da ação anti-inflamatória dos ácidos oleanólico e ursólico sobre as isoformas da ciclo-oxigenase por docking e dinâmica molecular

“…Anexa à referida cavidade, encontra-se uma cavidade polar circundada por His90, Gln192 e pelo resíduo da posição 513 (Histidina em COX-1, Arginina em COX-2), o que favorece a interação com grupos polares de ligantes em COX-2 porque o grupo guanidina de Arg513 é mais extenso que o anel imidazol de His513. 3,4 O desenvolvimento dos AINEs seletivos para COX-2, como celecoxibe (Celebra 1,5 A investigação da atividade COX-2-seletiva de novas moléculas naturais, sintéticas e semissintéticas, estruturalmente semelhantes ou não aos coxibes, continua, assim como a avaliação destas no tratamento de outras patologias como câncer e Mal de Alzheimer. 6 Considerando a biodiversidade brasileira, o pequeno número de estudos acerca do seu potencial farmacoterapêutico e a necessidade de se lançar no mercado outros fármacos COX-2 seletivos, tornase importante avaliar, in silico, a atividade inibitória de moléculas naturais sobre isoformas COX.…”