4D-QSAR analysis incorporates conformational and alignment freedom into the development of 3D-QSAR models for training sets of structure−activity data by performing ensemble averaging, the fourth “dimension”. The descriptors in 4D-QSAR analysis are the grid cell (spatial) occupancy measures of the atoms composing each molecule in the training set realized from the sampling of conformation and alignment spaces. Grid cell occupancy descriptors can be generated for any atom type, group, and/or model pharmacophore. A single “active” conformation can be postulated for each compound in the training set and combined with the optimal alignment for use in other molecular design applications including other 3D-QSAR methods. The influence of the conformational entropy of each compound on its activity can be estimated. Serial use of partial least-squares, PLS, regression and a genetic algorithm, GA, is used to perform data reduction and identify the manifold of top 3D-QSAR models for a training set. The unique manifold of 3D-QSAR models is arrived at by computing the extent of orthogonality in the residuals of error among the most significant 3D-QSAR models in the general GA population. Receptor independent (RI) 4D-QSAR analysis has been successfully applied to three training sets:  (a) benzylpyrimidine inhibitors of dihydrofolate reductase, (b) prostaglandin PGF2α antinidatory analogs, and, (c) dipyridodiazepinone inhibitors of HIV-1 reverse transcriptase (RT). Two general findings from these applications are that grid cell occupancy descriptors associated with the “constant” chemical structure of an analog series can be significant in the 3D-QSAR models and that there is an enormous data reduction in constructing 3D-QSAR models. The resultant 3D-QSAR models can be graphically represented by plotting the significant 3D-QSAR grid cells in space along with their descriptor attributes.

Nucleotide-binding domain leucine-rich repeat proteins (NLRs) play a key role in immunity and disease through their ability to modulate inflammation in response to pathogen-derived and endogenous danger signals. Here, we identify the requirements for activation of NLRP1, an NLR protein associated with a number of human pathologies, including vitiligo, rheumatoid arthritis, and Crohn disease. We demonstrate that NLRP1 activity is dependent upon ASC, which associates with the C-terminal CARD domain of NLRP1. In addition, we show that NLRP1 activity is dependent upon autolytic cleavage at Ser(1213) within the FIIND. Importantly, this post translational event is dependent upon the highly conserved distal residue His(1186). A disease-associated single nucleotide polymorphism near His(1186) and a naturally occurring mRNA splice variant lacking exon 14 differentially affect this autolytic processing and subsequent NLRP1 activity. These results describe key molecular pathways that regulate NLRP1 activity and offer insight on how small sequence variations in NLR genes may influence human disease pathogenesis.

Neomorphic mutations in isocitrate dehydrogenase 1 (IDH1) are driver mutations in acute myeloid leukemia (AML) and other cancers. We report the development of new allosteric inhibitors of mutant IDH1. Crystallographic and biochemical results demonstrated that compounds of this chemical series bind to an allosteric site and lock the enzyme in a catalytically inactive conformation, thereby enabling inhibition of different clinically relevant IDH1 mutants. Treatment of IDH1 mutant primary AML cells uniformly led to a decrease in intracellular 2-HG, abrogation of the myeloid differentiation block and induction of granulocytic differentiation at the level of leukemic blasts and more immature stem-like cells, in vitro and in vivo. Molecularly, treatment with the inhibitors led to a reversal of the DNA cytosine hypermethylation patterns caused by mutant IDH1 in AML patients’ cells. Our study provides proof-of-concept for the molecular and biological activity of novel allosteric inhibitors for targeting different mutant forms of IDH1 in leukemia.

The human, cytosolic enzyme isocitrate dehydrogenase 1 (IDH1) reversibly converts isocitrate to α-ketoglutarate (αKG). Cancer-associated somatic mutations in IDH1 result in a loss of this normal function but a gain in a new or neomorphic ability to convert αKG to the oncometabolite 2-hydroxyglutarate (2HG). To improve our understanding of the basis for this phenomenon, we have conducted a detailed kinetic study of wild-type IDH1 as well as the known 2HG-producing clinical R132H and G97D mutants and mechanistic Y139D and (newly described) G97N mutants. In the reductive direction of the normal reaction (αKG to isocitrate), dead-end inhibition studies suggest that wild-type IDH1 goes through a random sequential mechanism, similar to previous reports on related mammalian IDH enzymes. However, analogous experiments studying the reductive neomorphic reaction (αKG to 2HG) with the mutant forms of IDH1 are more consistent with an ordered sequential mechanism, with NADPH binding before αKG. This result was further confirmed by primary kinetic isotope effects for which saturating with αKG greatly reduced the observed isotope effect on (D)(V/K)NADPH. For the mutant IDH1 enzyme, the change in mechanism was consistently associated with reduced efficiencies in the use of αKG as a substrate and enhanced efficiencies using NADPH as a substrate. We propose that the sum of these kinetic changes allows the mutant IDH1 enzymes to reductively trap αKG directly into 2HG, rather than allowing it to react with carbon dioxide and form isocitrate, as occurs in the wild-type enzyme.