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A transition-state analogue inhibitor that covalently reversibly binds to an enzyme formally consists of two parts: the chemical site, CS and the recognition site, RS. We have experimentally and theoretically demonstrated that the trend of binding affinity in a series of isoselective inhibitors (with identical RS and different CS fragments) depends mainly on their CS fragments. Isoselective inhibitors have the same affinity trend toward different enzymes of the same family with a common catalytic mechanism. Thus, very good correlation between experimentally determined and theoretically calculated Ki values was demonstrated. A practical outcome is the application of the described method as a tool for an expert analysis in virtual screening of inhibitor libraries and in the design of new enzyme inhibitors.

Mechanistic studies of catalysis and the inhibition of serine and cysteine proteases afford new and sometimes surprising insights, challenging conventional dogmas in enzymology. The intrinsic source of the difference in the catalytic mechanisms of serine and cysteine hydrolases, the origin of the stability of the enzymeinhibitor complex in serine proteases, and the structures and mechanisms of catalysis and inhibition in cysteine proteases are not just intellectually interesting; our findings provide a mechanistic basis to understand the trend in the binding affinity of “warheads” of reversible covalent (reaction coordinate analogue, RCA) inhibitors. The theoretically derived covalent descriptors W1 and W2 differentiate serine and cysteine hydrolases and account for the energetic contribution of the new covalent bond in the enzymeinhibitor complex. The W1 and W2 descriptors are at the heart of our enzyme mechanism based method (EMBM); a new computer‐assisted drug design tool for the filtration of inhibitor warheads by activity. EMBM is unique because it accounts for both covalent and noncovalent interactions of RCA inhibitors with their target enzymes.

Pyruvate kinase (PK) M2 which catalyzes the last step in glycolysis, is the alternative spliced isoform expressed in cancer cells, and a key player in exerting the Warburg effect. One of the mechanisms by which PKM2 modulate cancer cell metabolism is by switching between the low activity monomer and the high activity tetramer forms. This process is controlled by the varying concentration of an upstream glycolytic intermediate, FBP. These changes enable the cancer cell to manage its usage of glucose carbon backbones, whether for ATP production or for biomass generation, according to its changing demands. Further, it has been recently shown that the elevated levels of ROS in cancer cells contribute to the decreased activity of PKM2 to support NADPH production to increase cellular anti-oxidation capacity to sustain proliferation. Our goal is to disrupt the metabolic adaptation of cancer cells with small molecule PKM2 modulators. We hypothesized that an activator will redirect the consumption of nutrients, especially of glucose, away from biomass production and ultimately send the cells to die. Using our proprietary structure-based technology, we identified several series of novel allosteric PKM2 activators. Chemical optimization resulted in potent compounds with AC50 as low as 10nM, which were selective against the other PK isoforms. These compounds were proven to stabilize the active tetramer form of PKM2 in cancer cells. Bioenergetic experiments in several cell lines demonstrated that not only do these agents reduce lactate production; they also reduce the oxygen consumption rate. Analysis of cell cycle showed that treatment with PKM2 activators causes the cells to arrest at the G1 phase. In outcome-based assays, these compounds significantly reduced the proliferation rate of various cancer cell lines, and this effect was sensitive to media conditions, such as glucose levels. Taken together, our data supports the hypothesis that activation of PKM2 effectively deprives the cancer cell of building blocks and reduces the detoxification capacity that are required to support growth and proliferation. An in vivo colorectal cancer HT29 cell line mouse xenograft model with a modestly active compound (IC50=0.9uM) demonstrated tumor growth inhibition greater than 50% (100 mg/kg Q2D and 200 and 400 mg/kg IP QD). The compound was very safe in mouse, even at the highest exposure levels (200 and 400 mg/kg IP QD), indicating that these efficacious doses are significantly lower than the MTD. Additional xenograft models are ongoing. Taken together, there is strong support for the effect of potent PKM2 small molecule activators on the cellular metabolism of cancer cells, demonstrating statistically significant anti-cancer effect in an animal model of colorectal cancer. The favorable DMPK profile of these compounds further supports their development as anti-proliferative agents, both as a single agent and in combination therapy. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3219. doi:1538-7445.AM2012-3219

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