NMR-assisted computational studies of peptidomimetic inhibitors bound in the hydrophobic pocket of HIV-1 glycoprotein 41

Due to the inherently flexible nature of a protein–protein interaction surface, it is difficult both to inhibit the association with a small molecule, and to predict how it might bind to the surface. In this study, we have examined small molecules that mediate the interaction between a WWI motif on the C-helix of HIV-1 glycoprotein-41 (gp41) and a deep hydrophobic pocket contained in the interior N-helical trimer. Association between these two components of gp41 leads to virus–cell and cell–cell fusion, which could be abrogated in the presence of an inhibitor that binds tightly in the pocket. We have studied a comprehensive combinatorial library of α-helical peptidomimetics, and found that compounds with strongly hydrophobic side chains had the highest affinity. Computational docking studies produced multiple possible binding modes due to the flexibility of both the binding site and the peptidomimetic compounds. We applied a transferred paramagnetic relaxation enhancement experiment to two selected members of the library, and showed that addition of a few experimental constraints enabled definitive identification of unique binding poses. Computational docking results were extremely sensitive to side chain conformations, and slight variations could preclude observation of the experimentally validated poses. Different receptor structures were required for docking simulations to sample the correct pose for the two compounds. The study demonstrated the sensitivity of predicted poses to receptor structure and indicated the importance of experimental verification when docking to a malleable protein–protein interaction surface.     

Ethynylphosphonamidates for the Rapid and Cysteine‐Selective Generation of Efficacious Antibody–Drug Conjugates

Requirements for novel bioconjugation reactions for the synthesis of antibody–drug conjugates (ADCs) are exceptionally high, since conjugation selectivity as well as the stability and hydrophobicity of linkers and payloads drastically influence the performance and safety profile of the final product. We report Cys‐selective ethynylphosphonamidates as new reagents for the rapid generation of efficacious ADCs from native non‐engineered monoclonal antibodies through a simple one‐pot reduction and alkylation. Ethynylphosphonamidates can be easily substituted with hydrophilic residues, giving rise to electrophilic labeling reagents with tunable solubility properties. We demonstrate that ethynylphosphonamidate‐linked ADCs have excellent properties for next‐generation antibody therapeutics in terms of serum stability and in vivo antitumor activity.     

Structure and dynamics of metallomacrocycles: recognition of zinc xylyl-bicyclam by an HIV coreceptor

As platforms for the design of metal-based therapeutic and diagnostic agents, macrocycles are rigid enough to provide strong metal binding sites and orient functional groups stereoselectively, yet flexible enough to accommodate structural changes required for induced-fit recognition of biological targets. We consider the recognition of the Zn(II) complex of the bis-tetraazamacrocycle xylyl-bicyclam, a potent anti-HIV agent, by the coreceptor CXCR4, a G-protein-coupled receptor used by HIV for membrane fusion and cell entry. NMR studies show that the macrocycles of Zn(II)(2)-xylyl-bicyclam perchlorate exist in aqueous solution as two major configurations, trans-I (nitrogen chirality R,S,R,S), and trans-III (S,S,R,R). Acetate addition induced a major structural change. X-ray crystallography shows that the acetate complex contains the unusual cis-V cyclam configuration (R,R,R,R and folded) with bidentate coordination of acetate to Zn(II) plus second-coordination-sphere double H-bond formation between diagonal NH protons on the opposite cyclam face and acetate carboxylate oxygens. Detailed 1D and 2D NMR studies show that the major configuration of Zn(II)(2)-xylyl-bicyclam acetate in aqueous solution is cis-V/trans-I. Molecular modeling shows that an analogous cis-V site can be formed when Zn(II)(2)-xylyl-bicyclam binds to CXCR4, involving the carboxylate groups of Asp262 (Zn(II) coordination) and Glu288 (double H-bonding). The second cyclam can adopt the trans-I (or trans-III) configuration with Zn(II) binding to Asp171. These interactions are consistent with the known structure-activity relationships for bicyclam anti-HIV activity and receptor mutation. Consideration of the anti-HIV activity of xylyl-bicyclam complexes of other metal ions suggests that affinity for carboxylates, configurational flexibility, and kinetic factors may all play roles in receptor recognition. For example, Pd(II) cyclam complexes interact only weakly with axial ligands and are inflexible and inactive, whereas Co(III) cyclams bind carboxylates strongly, are configurationally flexible, and yet have low activity. Our findings should aid the design of new generations of active macrocycles including highly specific chemokine receptor antagonists.     

Streptonigrin and lavendamycin partial structures. Preparation of 7-amino-2-(2′-pyridyl)quinoline-5,8-quinone-6′-carboxylic acid: A probe for the minimum,potent pharmacophore of the naturally occurring antitumor-antibiotics

The preparation of 7-amino-2-(2′-pyridyl)quinoline-5,8-quinone-6′-carboxylic acid (4) constituting a potential minimum, potent pharmacophore of streptonigrin (1) and lavendamycin (2) , two structurally-related naturally-occurring antitumor-antibiotic, is detailed. In contrast to observations associated with streptonigrin and lavendamycin in which the C-6′ acid potentiates the antitumor, antimicrobial, and cytotoxic activity of the naturally-occurring, substituted 7-aminoquinoline-5,8-quinone AB ring systems, the C-6′ carboxylic acid of 4 diminishes the observed antimicrobial and cytotoxic properties of 7-amino-2-(2′-pyridyl)quinoline-5,8-quinone.     

Synthesis of PI3K inhibitor GDC-0077 via a stereocontrolled N-arylation of α-amino acids

An efficient synthesis of PI3K inhibitor GDC-0077, featuring two consecutive Cu-catalyzed CN coupling reactions, is reported. The described synthetic route involves a chemoselective Ullmann-type coupling of a chiral difluoromethyl-substituted oxazolidinone, a Cu-catalyzed N-arylation of l-alanine with high stereochemical integrity, and a high-yielding final amide bond formation step to produce GDC-0077 in >99.5 area % HPLC purity.     

Effects of glucose,glutamine, and malate on the metabolism of spodoptera frugiperda clone 9 (sf9) cells

Optimal design and operation of bioreactors for insect cell culture is facilitated by functional relations providing quantitative information on cellular metabolite consumption kinetics, as well as on the specific cell growth rates (μ_G). Initial specific consumption rates of glucose, malate, and oxygen, and associated changes in μ_G, were measured forSpodoptera frugiperda clone 9 (Sf9) cells grown in batch suspension culture in medium containing 7–35 mM glucose, 0–16 mM malate, and 4–16 mM glutamine. The initial specific glucose consumption rate (q _G ) could be described by a modified Michaelis-Menten equation treating malate as a “competitive” inhibitorK ₁ = 6.5 mM) and glutamine as a “noncompetitive” inhibitorK _I = 14 mM) ofq _G , with aK _m of 7.1 mM for glucose. All three carbon sources were found to increase μ_G in a saturable manner, and a modified Monod equation was employed to describe this relationship (μ_Gmax = 0.047 h^-1). The initial specific oxygen consumption rate (q_O2) in Sf9 cells could be related to μ_G by the maintenance energy model, and it was calculated that, under typical culture conditions, about 15–20% of the cellular energy demand comes from functions not related to growth. Fitted parameters in mathematical expression for μg: K₄, Monod constant for glucose (mM); K₅, modified Monod constant for malate (mM); K₆, Monod constant for glutamine (mM); m_o2, specific consumption rate of oxygen by the cells under zero-growth conditions (nmol/cell/h); q_F, initial specific fumarate production rate (nmol/cell/ h);q _G , initial specific glucose consumption rate (nmol/cell/h); q_Gmax, maximum initial specific glucose consumption rate (nmol/cell/h);q _M , initial specific malate consumption rate (nmol/cell/h); q_o2, initial specific oxygen consumption rate (nmol/cell/h); Y_o2, cell yield on oxygen (cells/nmol); μ, initial specific cell growth rate (h^-1); μ_g, initial specific cell growth rate (h^-1); μG_max, maximum initial specific cell growth rate (h^-1).     

The products of the reaction of the hydroxyl radical with 2-ethoxyethyl acetate

The gas-phase reaction products of the OH radical with 2-ethoxyethyl acetate (EEA, CH₃C(O)OCH₂CH₂OCH₂CH₃) have been investigated. 1,2-Ethanediol acetate formate (EAF, CH₃C(O)OCH₂CH₂OC(O)H) and ethyl formate (EF, HC(O)OCH₂CH₃) were identified as the two main products. A third product, ethylene glycol diacetate (EGD, CH₃C(O)OCH₂CH₂OC(O)CH₃), was also observed. EAF, EF, and EGD formation yields were determined to be 0.37 ± 0.03 and 0.328 ± 0.018 and 0.040 ± 0.005, respectively. Proposed reaction mechanisms are discussed and compared with these data. © 1996 John Wiley & Sons, Inc.     

Frequency-Dependent Streaming Potentials

An experimental apparatus and data acquisition system was constructed to measure the streaming potential coupling coefficients as a function of frequency. The purpose of the experiments was to measure, for the first time, the real and imaginary portion of streaming potentials. In addition, the measured frequency range was extended beyond any previous measurements. Frequency-dependent streaming potential experiments were conducted on one glass capillary and two porous glass filters. The sample pore diameters ranged from 1 mm to 34 μm. Two frequency-dependent models (Packard and Pride) were compared to the data. Both Pride's and Packard's models have a good fit to the experimental data in the low- and intermediate-frequency regime. In the high-frequency regime, the data fit the theory after being corrected for capacitance effects of the experimental setup. Pride's generalized model appears to have the ability to more accurately estimate pore sizes in the porous medium samples. Packard's model has one unknown model parameter while Pride's model has four unknown model parameters, two of which can be independently determined experimentally. Pride's additional parameters may allow for a determination of permeability. Copyright 2001 Academic Press.