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Mass spectrometry (MS)-based protein footprinting, a valuable structural tool in mapping protein-ligand interaction, has been extensively applied to protein-protein complexes, showing success in mapping large interfaces. Here, we utilized an integrated footprinting strategy incorporating both hydrogen-deuterium exchange (HDX) and hydroxyl radical footprinting (i.e., fast photochemical oxidation of proteins (FPOP)) for molecular-level characterization of the interaction of human bromodomain-containing protein 4 (BRD4) with a hydrophobic benzodiazepine inhibitor. HDX does not provide strong evidence for the location of the binding interface, possibly because the shielding of solvent by the small molecule is not large. Instead, HDX suggests that BRD4 appears to be stabilized by showing a modest decrease in dynamics caused by binding. In contrast, FPOP points to a critical binding region in the hydrophobic cavity, also identified by crystallography, and, therefore, exhibits higher sensitivity than HDX in mapping the interaction of BRD4 with compound 1. In the absence or under low concentrations of the radical scavenger, FPOP modifications on Met residues show significant differences that reflect the minor change in protein conformation. This problem can be avoided by using a sufficient amount of proper scavenger, as suggested by the FPOP kinetics directed by a dosimeter of the hydroxyl radical.

We describe an integrated approach of using hydrogen–deuterium exchange mass spectrometry (HDX-MS), chemical cross-linking mass spectrometry (XL-MS), and molecular docking to characterize the bindi...

The hepatitis C virus (HCV) NS5B replicase is a prime target for the development of direct-acting antiviral drugs for the treatment of chronic HCV infection. Inspired by the overlay of bound structures of three structurally distinct NS5B palm site allosteric inhibitors, the high-throughput screening hit anthranilic acid 4, the known benzofuran analogue 5, and the benzothiadiazine derivative 6, an optimization process utilizing the simple benzofuran template 7 as a starting point for a fragment growing approach was pursued. A delicate balance of molecular properties achieved via disciplined lipophilicity changes was essential to achieve both high affinity binding and a stringent targeted absorption, distribution, metabolism, and excretion profile. These efforts led to the discovery of BMS-929075 (37), which maintained ligand efficiency relative to early leads, demonstrated efficacy in a triple combination regimen in HCV replicon cells, and exhibited consistently high oral bioavailability and pharmacokinetic parameters across preclinical animal species. The human PK properties from the Phase I clinical studies of 37 were better than anticipated and suggest promising potential for QD administration.

HIV-1 maturation inhibition (MI) has been clinically validated as an approach to the control of HIV-1 infection. However, identifying an MI with both broad polymorphic spectrum coverage and good oral exposure has been challenging. Herein, we describe the design, synthesis, and preclinical characterization of a potent, orally active, second generation HIV-1 MI, BMS-955176 (2), which is currently in Phase IIb clinical trials as part of a combination antiretroviral regimen.

Electron deficient, bivalent sulfur atoms have two areas of positive electrostatic potential, a consequence of the low-lying σ* orbitals of the C-S bond that are available for interaction with electron donors including oxygen and nitrogen atoms and, possibly, π-systems. Intramolecular interactions are by far the most common manifestation of this effect, which offers a means of modulating the conformational preferences of a molecule. Although a well-documented phenomenon, a priori applications in drug design are relatively sparse and this interaction, which is often isosteric with an intramolecular hydrogen-bonding interaction, appears to be underappreciated by the medicinal chemistry community. In this Perspective, we discuss the theoretical basis for sulfur σ* orbital interactions and illustrate their importance in the context of drug design and organic synthesis. The role of sulfur interactions in protein structure and function is discussed and although relatively rare, intermolecular interactions between ligand C-S σ* orbitals and proteins are illustrated.

Described herein are structure-activity relationship studies that resulted in the optimization of the activity of members of a class of cyclopropyl-fused indolobenzazepine HCV NS5B polymerase inhibitors. Subsequent iterations of analogue design and syntheses successfully addressed off-target activities, most notably human pregnane X receptor (hPXR) transactivation, and led to significant improvements in the physicochemical properties of lead compounds. Those analogues exhibiting improved solubility and membrane permeability were shown to have notably enhanced pharmacokinetic profiles. Additionally, a series of alkyl bridged piperazine carboxamides was identified as being of particular interest, and from which the compound BMS-791325 (2) was found to have distinguishing antiviral, safety, and pharmacokinetic properties that resulted in its selection for clinical evaluation.

A series of conformationally restricted homotryptamines has been synthesized and shown to be potent inhibitors of hSERT. Conformational restriction of the homotryptamine side chain was attained by the insertion of a cyclopentyl ring, with the indole ring and the terminal dialkylamino group occupying the 1- and 3-positions, respectively. Nitrile and fluoro substitutions at the indole 5-position gave highest hSERT potency. Preferred cyclopentane ring stereochemistry in both series was cis (I S,3R for 5-CN compound 8a, 1 R,3S for 5-F compound 9a). High hSERT binding affinity was observed for 8a and 9a (0.22 and 0.63 nM, respectively). The corresponding trans isomers were 4—9 times less potent. 8a, dosed at 1 and 3 mg/kg po, produced a robust, dose-dependent increase in extracellular serotonin in the frontal cortex of rats, similar to that induced by paroxetine at 5 mg/kg, po. By contrast, 9a did not produce a significant increase in extracellular serotonin in rat frontal cortex at 3 mg/kg po due to relatively low brain and plasma levels.

A series of indole cyclopropylmethylamines were found to be potent serotonin reuptake inhibitors. Nitrile substituents at the 5 and 7 positions of the indole ring gave high affinity for hSERT, and the preferred cyclopropane stereochemistry was determined to be (1S,2S)-trans. The cis-cyclopropanes had 20- to 30-fold less affinity than the trans, and the preferred cis stereochemistry was (1R,2S)-cis. Substitution of the indole N-1 position with methyl or ethyl groups gave a 10- to 30-fold decrease in affinity for hSERT, suggesting either a hydrogen-bonding interaction or limited steric tolerance in the region of the indole nitrogen. Compound (+)-12a demonstrated potent hSERT binding (Ki = 0.18 nM) in vitro and was more than 1000-fold less potent at hDAT, hNET, 5-HT1A, and 5-HT6. In vivo, (+)-12a produced robust, dose-dependent increases in extracellular serotonin in rat frontal cortex typical of a selective serotonin reuptake inhibitor. The maximal response produced by (+)-12a was similar to that of fluoxetine but at an approximately 10-fold lower dose.

B3LYP/6-31G* calculations have been performed on the chair Cope rearrangements of a wide variety of 1,5-hexadienes, substituted with cyano or with vinyl groups. In agreement with experimental data from the study of phenyl substituent effects, cyano and vinyl groups at C(2) and C(5) are found to provide cooperative lowering of the activation enthalpy, as are substituents at C(1), C(3), C(4), and C(6). In contrast, the stabilization of the transition structure by substituents at C(2) and C(4) or at C(1), C(3), and C(5) is predicted to be competitive, rather than cooperative. These findings are consistent with what Doering has termed a chameleonic transition state for the Cope rearrangement, one in which the relative importance of the cyclohexane-1,4-diyl and bis-allyl radical resonance contributors can be altered by substituents, depending on the carbons to which the substituents are attached. The computed bond lengths in the transition structures and the calculated and experimentally observed kinetic isoto...

The potential energy surfaces for the thermal reactions of bicyclo[3.2.0]hept-2-ene and norbornene have been explored with density functional theory at the Becke3LYP/6-31G* level. Both concerted and diradical pathways for the retro-Diels−Alder reaction of norbornene have been examined, and the activation parameters and 13C primary kinetic isotope effects predicted for the concerted pathway are in excellent agreement with experimental data. The concerted mechanism is favored over the lowest energy stepwise diradical route by 12.4 kcal/mol. For the orbital symmetry-allowed suprafacial-inversion (si) pathway of the [1,3] sigmatropic rearrangement of bicyclo[3.2.0]hept-2-ene to form norbornene, a mechanism involving a transition state which leads to a broad diradical plateau on the potential energy surface is predicted. Implications of these surfaces, which differ substantially from those obtained by semiempirical calculations, are also discussed.

The mechanisms of the degenerate [5,5] sigmatropic rearrangements of 5,5a,10,10a-tetrahydroheptalene and (Z,Z)-1,3,7,9-decatetraene were explored with restricted and unrestricted Becke3LYP/6-31G* hybrid HF-DFT calculations. The restricted DFT wavefunctions for the synchronous, concerted transition structures for these formally Woodward−Hoffmann allowed 10-electron rearrangements are unstable with respect to unrestricted wavefunctions. A stepwise diradical mechanism is predicted for both reactions. The 9 kcal/mol preference for the [5s,5s] mechanism over the [5a,5a] pathway in the rearrangement of decatetraene results primarily from the geometric distortions that the system must adopt in the [5a,5a] transition structure. The geometric and electronic characteristics of the [5,5] and [3,3] (Cope) rearrangements are compared.

The (2+2) cycloadditions of SO3 to ethene, propene, and 2-methylpropene were investigated with Hartree−Fock, MP2, QCISD(T), and hybrid Hartree−Fock/density functional theory (HF-DFT) methods. Exper...

Experimental activation parameters for the intramolecular Diels−Alder reactions of 1,3,8-nonatriene, 1,3,9-decatriene, and 1,3,10-undecatriene have been measured, and the Monte Carlo-Jumping between Wells/Stochastic Dynamics [MC(JBW)/SD] method, which gives relative free energies of activation, was tested as a means to predict stereoselectivities. The predictions are compared to experimental results, and to predictions from quantum and molecular mechanics methods.