Organocuprate Conjugate Addition: The Square-Planar “Cu^III” Intermediate

Rapid-injection NMR experiments with 2-cyclohexenone, TMSCl, and Me2CuLi•LiCN by the Bertz and Ogle team (Bertz, S. H.; Cope, S.; Murphy, M.; Ogle, C. A.; Taylor, B. J. J. Am. Chem. Soc. 2007, 129, 7208−7209) have led to the observation of a new product-forming conjugate addition intermediate characterized by 1H and 13C NMR at −100 °C. By employing conformational analysis, density functional theory (DFT) optimization, and prediction of NMR observables (δ (TMS), 2J), the structure of the observed species is confirmed to be the elusive and long sought tetracoordinate square-planar “Cu(III) intermediate”. Additional calculations suggest that symmetrical or unsymmetrical tetraalkyl analogues ([R4Cu]-1) are inherently more stable than the CN analogues ([R3CuCN]-1) and may be isolable

Models for Predicting IKKA and IKKB Blockade

We describe the application of different methods in the development of QSAR models for IKKA and IKKB inhibition. The results show that the best QSAR models provide highly accurate predictions for existing IkB-kinase (IKK) inhibitors. The exceptions, corresponding to 5% of the known collection of inhibitors, are five classes of compounds incorporating the nitrile or sulfonamide moieties, small compounds with molecular weights of less than 300, and two classes of blockers considered to be type II kinase inhibitors. Comparison of our novel IKKB homology model and the recently reported IKKB crystal structure implies that a predictive protein–antagonist complex structure is more likely to exist as an inactive form in the crystalline state as observed in the recent protein X-ray structure

Models for Predicting IKKA and IKKB Blockade

We describe the application of different methods in the development of QSAR models for IKKA and IKKB inhibition. The results show that the best QSAR models provide highly accurate predictions for existing IkB-kinase (IKK) inhibitors. The exceptions, corresponding to 5% of the known collection of inhibitors, are five classes of compounds incorporating the nitrile or sulfonamide moieties, small compounds with molecular weights of less than 300, and two classes of blockers considered to be type II kinase inhibitors. Comparison of our novel IKKB homology model and the recently reported IKKB crystal structure implies that a predictive protein–antagonist complex structure is more likely to exist as an inactive form in the crystalline state as observed in the recent protein X-ray structure

The Quest for a Simple Bioactive Analog of Paclitaxel as a Potential Anticancer Agent

ConspectusPaclitaxel (PTX), introduced into the clinic in 1991, has revealed itself as an effective antimicrotubule drug for treatment of a range of otherwise intractable cancers. Along with docetaxel (DTX) and in combination with other agents such as cisplatin, it has proven to be a first-line therapy. Unfortunately, PTX and DTX carry severe liabilities such as debilitating side effects, rapid onset of resistance, and rather complex molecular structures offering substantial challenges to ease of synthetic manipulation. Consequently, the past 15 years has witnessed many efforts to synthesize and test highly modified analogs based on intuitive structural similarity relationships with the PTX molecular skeleton, as well as efforts to mimic the conformational profile of the ligand observed in the macromolecular tubulin–PTX complex.Highly successful improvements in potency, up to 50-fold increases in IC₅₀, have been achieved by constructing bridges between distal centers in PTX that imitate the conformer of the electron crystallographic binding pose. Much less successful have been numerous attempts to truncate PTX by replacing the baccatin core with simpler moieties to achieve PTX-like potencies and applying a wide range of flexible synthesis-based chemistries. Reported efforts, characterized by a fascinating array of baccatin substitutes, have failed to surpass the bioactivities of PTX in both microtubule disassembly assays and cytotoxicity measurements against a range of cell types. Most of the structures retain the main elements of the PTX C13 side chain, while seeking a smaller rigid bicycle as a baccatin replacement adorned with substituents to mimic the C2 benzoyl moiety and the oxetane ring.We surmise that past studies have been handicapped by solubility and membrane permeability issues, but primarily by the existence of an expansive taxane binding pocket and the discrepancy in molecular size between PTX and the pruned analogs. A number of these molecules offer molecular volumes 50–60% that of PTX, fewer contacts with the tubulin protein, severe mismatches with the PTX pharmacophore, lessened capacity to dispel binding site waters contributing to Δ<i>G</i>_bind, and unanticipated binding poses. The latter is a critical drawback if molecular designs of simpler PTX structures are based on a perceived or known PTX binding conformation. We conclude that design and synthesis of a highly cytotoxic tubulin-assembly agent based on the paclitaxel pharmacophore remains an unsolved challenge, but one that can be overcome by focus on the architecture of the taxane binding site independent of the effective, but not unique, hand-in-glove match represented by the PTX–tubulin complex

The Tubulin-Bound Conformation of Paclitaxel: T-Taxol vs “PTX-NY”

Nearly 35 years after its discovery and 11 years after FDA approval of paclitaxel (PTX) as a breakthrough anticancer drug, the 3-D structure of the agent bound to its β-tubulin target was proposed to be T-Taxol. The latter bioactive form has recently been challenged by the Ojima group with a structure, “PTX-NY” (“REDOR Taxol”), in which the C-13 side chain is proposed to adopt a different conformation and an alternative hydrogen-bonding pattern in the tubulin binding site. Previously, the two conformers were compared to show that only T-Taxol fits the PTX-derived electron crystallographic density. That work has been extended by molecular mechanics and quantum chemical methods to reveal that the PTX-NY conformation is relatively less stable, on average, by 10−11 kcal/mol. In agreement with NMR studies, an 11 ns molecular dynamics treatment for PTX in an explicit water pool locates T-Taxol along the trajectory, but not PTX-NY. Docking of various PTX conformers into the electron crystallographic binding site of tubulin demonstrates that PTX-NY cannot be accommodated unless the pocket is reorganized in violation of the experimental constraints. Finally, analysis of the structures of T-Taxol and PTX-NY for their capacity to predict the existence of superpotent PTX analogues discloses that only the former forecasts such analogues, as now established by the T-Taxol-inspired synthesis of bridged taxanes. In sum, all empirical criteria support T-Taxol as the bound conformation of PTX on β-tubulin in microtubules

¹³C Kinetic Isotope Effects for the Addition of Lithium Dibutylcuprate to Cyclohexenone. Reductive Elimination Is Rate-Determining

13C Kinetic Isotope Effects for the Addition of Lithium Dibutylcuprate to Cyclohexenone. Reductive Elimination Is Rate-Determinin

Mechanism of Chorismate Mutase: Contribution of Conformational Restriction to Catalysis in the Claisen Rearrangement

The mechanism of the enzyme- and antibody-catalyzed Claisen rearrangement of chorismate to prephenate was investigated experimentally on model compounds and by using quantum chemistry calculations at the Becke3LYP/6-31G* level of theory. Conformational restriction of the allyl vinyl ether fragment to the reactive chairlike conformation in 1 induces a 2 × 105-fold rate acceleration (ΔΔG⧧ = 7.3 kcal/mol) of the Claisen rearrangement in C6D6 relative to an unrestricted analogue 3. A direct relationship between activation barrier lowering and the distance between reactive termini has been observed in additional model systems. Compression of the reactive centers from 4.0 to 3.0 Å results in a barrier lowering from 24 kcal/mol to 12 kcal/mol in one conformationally restricted model. Further compression reduces the activation barrier to a mere 4 kcal/mol. Rearrangement rate increases via conformational restriction and reactive center compression derive mainly from ground-state destabilization in which entropic factors do not contribute significantly. The chorismate mutase mechanism is rationalized as a series of three steps involving (1) capture of the unstable pseudo-diaxial conformer of chorismate in a chairlike geometry (<3 kcal/mol contribution to barrier lowering); (2) further confinement of the reacting termini with a potential for >10 kcal/mol barrier reduction; and (3) rearrangement accompanied by additional transition-state stabilization from ionic H-bonding at the ether oxygen. Since the total barrier lowering is greater than that required to account for the observed 3 × 106-fold enzymatic catalysis, the rearrangement itself is probably not the rate-determining step. The major contribution to catalysis could, in principle, come from confining the reactive centers to contact distances, a conclusion consistent with the spatiotemporal precept

Mechanism of Chorismate Mutase: Contribution of Conformational Restriction to Catalysis in the Claisen Rearrangement

The mechanism of the enzyme- and antibody-catalyzed Claisen rearrangement of chorismate to prephenate was investigated experimentally on model compounds and by using quantum chemistry calculations at the Becke3LYP/6-31G* level of theory. Conformational restriction of the allyl vinyl ether fragment to the reactive chairlike conformation in 1 induces a 2 × 105-fold rate acceleration (ΔΔG⧧ = 7.3 kcal/mol) of the Claisen rearrangement in C6D6 relative to an unrestricted analogue 3. A direct relationship between activation barrier lowering and the distance between reactive termini has been observed in additional model systems. Compression of the reactive centers from 4.0 to 3.0 Å results in a barrier lowering from 24 kcal/mol to 12 kcal/mol in one conformationally restricted model. Further compression reduces the activation barrier to a mere 4 kcal/mol. Rearrangement rate increases via conformational restriction and reactive center compression derive mainly from ground-state destabilization in which entropic factors do not contribute significantly. The chorismate mutase mechanism is rationalized as a series of three steps involving (1) capture of the unstable pseudo-diaxial conformer of chorismate in a chairlike geometry (<3 kcal/mol contribution to barrier lowering); (2) further confinement of the reacting termini with a potential for >10 kcal/mol barrier reduction; and (3) rearrangement accompanied by additional transition-state stabilization from ionic H-bonding at the ether oxygen. Since the total barrier lowering is greater than that required to account for the observed 3 × 106-fold enzymatic catalysis, the rearrangement itself is probably not the rate-determining step. The major contribution to catalysis could, in principle, come from confining the reactive centers to contact distances, a conclusion consistent with the spatiotemporal precept

Diastereoselective Addition of Chlorotitanium Enolate of <i>N</i>-Acyl Thiazolidinethione to <i>O</i>-Methyl Oximes: A Novel, Stereoselective Synthesis of α,β-Disubstituted β-Amino Carbonyl Compounds via Chiral Auxiliary Mediated Azetine Formation

We have discovered a novel and highly diastereoselective synthesis of azetinyl thiazolidine-2-thiones that utilizes additions of the chlorotitanium enolates of N-acyl thiazolidin-2-thiones to O-methyl aldoximes. The “anti” azetines can be subsequently converted to the corresponding α,β-disubstituted β-amino carbonyl compound with retention of stereochemistry. The formation of azetine and the product of its “hydrolytic” opening has been confirmed by X-ray crystallographic analyses

T-Taxol and the Electron Crystallographic Density in β-Tubulin

T-Taxol has been proposed as the bioactive conformation on β-tubulin and subsequently utilized in the design of a series of highly active bridged taxane analogues. A modified T-form with a reversed C-13 side chain orientation has recently been proposed as an equally plausible bioactive shape. A comparison of the two spatial alternatives within the tubulin binding site electron crystallographic density suggests strongly that T-Taxol is the bioactive conformation