Strategies to Stabilize Dalbavancin in Aqueous Solutions; Section-1: the Effects of Metal Ions and Buffers.

PURPOSE: The effect of monovalent (Na+ and K+) and divalent (Ca2+, Mg2+, and Zn2+) metal ions combined with citrate or acetate buffers (pH 4.5) on the stability of dalbavancin in aqueous solutions was investigated. METHOD: RP-HPLC and HP-SEC were used to evaluate the stability of aqueous solutions of dalbavancin in different combinations of buffers and metal ions after four weeks of storage at 5°C and 55°C. A long-term study of formulations with divalent metal ions was conducted over six months at 5°C., 25°C and 40°C using RP-HPLC. RESULTS: All formulations in citrate buffered solutions precipitated. Dalbavancin solutions in 10 mM acetate buffer at 55°C were more stable in 10 mM CaCl2, 5 mM ZnCl2 and 10 mM MgCl2 than those containing 2 mM NaCl or 5 mM KCl, although the MgCl2 formulations precipitated slightly. No significant effect was observed for any of the divalent metal ions at 40°C for six months. CONCLUSION: Dalbavancin's stability in solution was improved by a combination of acetate and divalent metal ions at 55°C for four weeks. No effect was observed with acetate or metal ions alone, and no effect was observed after six months at 40°C suggesting that acetate and divalent metal ions together interact with dalbavancin via a thermally activated step to inhibit hydrolysis of the drug.

Strategies To Stabilize Dalbavancin in Aqueous Solutions; Section 3: The Effects of 2 Hydroxypropyl-ß-Cyclodextrin and Phosphate Buffer with and without Divalent Metal Ions.

PURPOSE: New formulations of the glycopeptide drug dalbavancin containing 2-hydroxpropyl-ß-cyclodextrin (2HPßCD) with or without divalent metal ions in phosphate buffer (pH 7.0) were tested to evaluate whether these excipients influence the aqueous solution stability of dalbavancin. METHOD: Recovery of dalbavancin from phosphate buffered solutions at pH 7.0 with different concentrations of 2HPßCD and a divalent metal ion (Ca2+, Mg2+, or Zn2+) was evaluated by RP-HPLC and HP-SEC after four weeks of storage at 5°C and 55°C. A long-term study of formulations with 2HPßCD and Mg2+ was carried out over six months at 5°C, 25°C, and 40°C using RP-HPLC. RESULTS: Dalbavancin solutions with either 5.5 mM or 55 mM 2HPßCD were significantly more stable with Mg2+ than with the other divalent metal ions, both at 55°C for four weeks and at 40°C for six months. Dalbavancin was found to be more stable in aqueous solutions at a concentration of 1 mg/mL than at 20 mg/mL with 2HPßCD and Mg2+ at 40°C for six months. CONCLUSION: The results suggest that 2HPßCD forms an inclusion complex with dalbavancin that slows the formation of the major degradant, mannosyl aglycone (MAG). The effect of 2HPßCD is increased in the presence of Mg2+ and phosphate at pH 7.0, and the complex is more stable at a dalbavancin concentration of 1 mg/mL than at 20 mg/mL. These observations point towards the possibility of formulating a dalbavancin injection solution with a long shelf life at room temperature and physiological pH.

A Systematic Degradation Kinetics Study of Dalbavancin Hydrochloride Injection Solutions.

The degradation kinetics of the glycopeptide antibiotic dalbavancin in solution are systematically evaluated over the pH range 1-12 at 70°C. The decomposition rate of dalbavancin was measured as a function of pH, buffer composition, temperature, ionic strength, and drug concentration. A pH-rate profile was constructed using pseudo first-order kinetics at 70°C after correcting for buffer effects; the observed pH-rate profile could be fitted with standard pseudo first order rate laws. The degradation reactions of dalbavancin were found to be strongly dependent on pH and were catalyzed by protons or hydroxyl groups at extreme pH values. Dalbavancin shows maximum stability in the pH region 4-5. Based on the Arrhenius equation, dalbavancin solution at pH 4.5 is predicted to have a maximum stability of thirteen years under refrigerated conditions, eight months at room temperature and one month at 40°C. Mannosyl Aglycone (MAG), the major thermal and acid degradation product, and DB-R6, an additional acid degradation product, were formed in dalbavancin solutions at 70°C due to hydrolytic cleavage at the anomeric carbons of the sugars. Through deamination and hydrolytic cleavage of dalbavancin, a small amount of DB-Iso-DP2 (RRT-1.22) degradation product was also formed under thermal stress at 70°C. A greater amount of the base degradation product DB-R2 forms under basic conditions at 70°C due to epimerization of the alpha carbon of phenylglycine residue 3.

Glycopeptide antibiotic drug stability in aqueous solution.

Glycopeptide antimicrobials are a class of naturally occurring or semi-synthetic glycosylated products that have shown antibacterial activity against gram-positive organisms by inhibiting cell-wall synthesis. In most cases, these drugs are prepared in dry powder (lyophilized) form due to chemical and physical instability in aqueous solution; however, from an economic and practical point of view, liquid formulations are preferred. Researchers have recently found ways to formulate some glycopeptide antibiotic therapeutic drugs in aqueous solution at refrigerated or room temperature. Chemical degradation can be significantly slowed by formulating them at a defined pH with specific buffers, avoiding oxygen reactive species, and minimizing solvent exposure. Sugars, amino acids, polyols, and surfactants can reduce physical degradation by restricting glycopeptide mobility and reducing solvent interaction. This review focuses on recent studies on glycopeptide antibiotic drug stability in aqueous solution. It is organized into three sections: (i) glycopeptide antibiotic instability due to chemical and physical degradation, (ii) strategies to improve glycopeptide antibiotic stability in aqueous solution, and (iii) a survey of glycopeptide antibiotic drugs currently available in the market and their stability based on published literature and patents. Antimicrobial resistance deaths are expected to increase by 2050, making heat-stable glycopeptides in aqueous solution an important treatment option for multidrug-resistant and extensively drug-resistant pathogens. In conclusion, it should be possible to formulate heat stable glycopeptide drugs in aqueous solution by understanding the degradation mechanisms of this class of therapeutic drugs in greater detail, making them easily accessible to developing countries with a lack of cold chains.

Altering the N-terminal arms of the polymerase manager protein UmuD modulates protein interactions.

Escherichia coli cells that are exposed to DNA damaging agents invoke the SOS response that involves expression of the umuD gene products, along with more than 50 other genes. Full-length UmuD is expressed as a 139-amino-acid protein, which eventually cleaves its N-terminal 24 amino acids to form UmuD'. The N-terminal arms of UmuD are dynamic and contain recognition sites for multiple partner proteins. Cleavage of UmuD to UmuD' dramatically affects the function of the protein and activates UmuC for translesion synthesis (TLS) by forming DNA Polymerase V. To probe the roles of the N-terminal arms in the cellular functions of the umuD gene products, we constructed additional N-terminal truncated versions of UmuD: UmuD 8 (UmuD Δ1-7) and UmuD 18 (UmuD Δ1-17). We found that the loss of just the N-terminal seven (7) amino acids of UmuD results in changes in conformation of the N-terminal arms, as determined by electron paramagnetic resonance spectroscopy with site-directed spin labeling. UmuD 8 is cleaved as efficiently as full-length UmuD in vitro and in vivo, but expression of a plasmid-borne non-cleavable variant of UmuD 8 causes hypersensitivity to UV irradiation, which we determined is the result of a copy-number effect. UmuD 18 does not cleave to form UmuD', but confers resistance to UV radiation. Moreover, removal of the N-terminal seven residues of UmuD maintained its interactions with the alpha polymerase subunit of DNA polymerase III as well as its ability to disrupt interactions between alpha and the beta processivity clamp, whereas deletion of the N-terminal 17 residues resulted in decreases in binding to alpha and in the ability to disrupt the alpha-beta interaction. We find that UmuD 8 mimics full-length UmuD in many respects, whereas UmuD 18 lacks a number of functions characteristic of UmuD.

CW-EPR Spectral Simulations: Slow-Motion Regime.

This chapter reviews the range of methods currently available for calculating the electron paramagnetic resonance (EPR) spectrum of nitroxide spin-labeled biomolecules undergoing slow motion. The two major approaches include the stochastic Liouville equation (SLE) which represents the spin label motion using diffusion operators, and the dynamic trajectory (DT) approach, which enables the EPR spectrum to be calculated from molecular dynamics simulations. The basic model parameters needed for each approach are described, together with a broad outline of the theoretical approaches underlying the methods, sufficient to allow their comparison for different applications. Hybrid methods utilizing a combination of SLE and DT approaches are briefly discussed.

Effect of ingested lipids on drug dissolution and release with concurrent digestion: a modeling approach.

PURPOSE: To mechanistically study and model the effect of lipids, either from food or self-emulsifying drug delivery systems (SEDDS), on drug transport in the intestinal lumen. METHODS: Simultaneous lipid digestion, dissolution/release, and drug partitioning were experimentally studied and modeled for two dosing scenarios: solid drug with a food-associated lipid (soybean oil) and drug solubilized in amodel SEDDS (soybean oil and Tween 80 at 1:1 ratio). Rate constants for digestion, permeability of emulsion droplets, and partition coefficients in micellar and oil phases were measured, and used to numerically solve the developed model. RESULTS: Strong influence of lipid digestion on drug release from SEDDS and solid drug dissolution into food-associated lipid emulsion was observed and predicted by the developed model. Ninety minutes after introduction of SEDDS, there was 9% and 70% drug release in the absence and presence of digestion, respectively. However, overall drug dissolution in the presence of food-associated lipids occurred over a longer period than without digestion. CONCLUSION: A systems-based mechanistic model incorporating simultaneous dynamic processes occurring upon dosing of drug with lipids enabled prediction of aqueous drug concentration profile. This model, once incorporated with a pharmacokinetic model considering processes of drug absorption and drug lymphatic transport in the presence of lipids, could be highly useful for quantitative prediction of impact of lipids on bioavailability of drugs.

Synthesis of a spin-labeled anti-estrogen as a dynamic motion probe for the estrogen receptor ligand binding domain.

The preparation and characterization of a novel nitroxide spin probe based on a steroidal anti-estrogen is described. The probe 5 demonstrated very high binding affinity for both the alpha and beta isoforms of the estrogen receptor-ligand binding domain. EPR spectrometric studies demonstrate conformational constraints for the ligand, consistent with the nitroxyl moiety occupying a position just beyond the receptor-solvent interface.

Electron spin labeling reveals the highly dynamic N-terminal arms of the SOS mutagenesis protein UmuD.

Electron paramagnetic resonance (EPR) spectroscopy was used to probe the conformational dynamics of the N-terminal arms of the umuD gene products. We determined that the arms of UmuD(2) display a large degree of motion, are largely unbound from the globular C-terminal domain, and that the free energy of dissociation is +2.1 kJ mol(-1).

Modeling the human intestinal mucin (MUC2) C-terminal cystine knot dimer.

Intestinal mucus, a viscous secretion that lines the mucosa, is believed to be a barrier to absorption of many therapeutic compounds and carriers, and is known to play an important physiological role in controlling pathogen invasion. Nevertheless, there is as yet no clear understanding of the barrier properties of mucus, such as the nature of the molecular interactions between drug molecules and mucus components as well as those that govern gel formation. Secretory mucins, large and complex glycoprotein molecules, are the principal determinants of the viscoelastic properties of intestinal mucus. Despite the important role that mucins play in controlling transport and in diseases such as cystic fibrosis, their structures remain poorly characterized. The major intestinal secretory mucin gene, MUC2, has been identified and fully sequenced. The present study was undertaken to determine a detailed structure of the cysteine-rich region within the C-terminal end of human intestinal mucin (MUC2) via homology modeling, and explore possible configurations of a dimer of this cysteine-rich region, which may play an important role in governing mucus gel formation. Based on sequence-structure alignments and three-dimensional modeling, a cystine knot tertiary structure homologous to that of human chorionic gonadotropin (HCG) is predicted at the C-terminus of MUC2. Dimers of this C-terminal cystine knot (CTCK) were modeled using sequence alignment based on HCG and TGF-beta, followed by molecular dynamics and simulated annealing. Results support the formation of a cystine knot dimer with a structure analogous to that of HCG.

Investigation of water and methanol sorption in monovalent- and multivalent-ion-exchanged nafion membranes using electron spin resonance.

Electron spin resonance (ESR) spectroscopy was used to monitor the local environment of 2,2,6,6-tetramethyl-4-piperidone N-oxide (TEMPONE) spin probe in Li(+), Ca(2+), and Al(3+) ion-exchanged Nafion 117 membranes swollen with mixed methanol/water solvent at varying compositions. The (14)N hyperfine splitting, a(N), which reflects the local polarity of the nitroxide probe, remains nearly steady at higher solvent contents but increases substantially at lower solvent contents, reflecting close contact with the ions. The rotational rate (R) of the probe increased with solvent content, depending strongly on the amount of solvent at low contents but increasing more gradually at higher solvent contents, similar to the behavior of previously measured solvent translation diffusion coefficients. The rotational rate data from water-containing membranes were fitted using the Fujita free-volume diffusion model, which indicated that multivalent ions tend to increase the free volume fraction of the polymer while decreasing that of the solvent phase. Methanol-containing membranes exhibited greater variation with different exchange ions, but the data could not be fit using the free-volume model, suggesting that the assumption of two phases underlying the free-volume model might not apply to this case. The difference in the trends of swelling between water and methanol is consistent with previous results that have indicated different patterns of penetration for the two solvents. The results are interpreted in terms of changes in membrane morphology with higher-valence ions.

Dynamic conformational responses of a human cannabinoid receptor-1 helix domain to its membrane environment.

The influence of membrane environment on human cannabinoid 1 (hCB(1)) receptor transmembrane helix (TMH) conformational dynamics was investigated by solid-state NMR and site-directed spin labeling/EPR with a synthetic peptide, hCB(1)(T377-E416), corresponding to the receptor's C-terminal component, i.e., TMH7 and its intracellular alpha-helical extension (H8) (TMH7/H8). Solid-state NMR experiments with mechanically aligned hCB(1)(T377-E416) specifically (2)H- or (15)N-labeled at Ala380 and reconstituted in membrane-mimetic dimyristoylphosphocholine (DMPC) or 1-palmitoyl-2-oleoyl-sn-glycerophosphocholine (POPC) bilayers demonstrate that the conformation of the TMH7/H8 peptide is more heterogeneous in the thinner DMPC bilayer than in the thicker POPC bilayer. As revealed by EPR studies on hCB(1)(T377-E416) spin-labeled at Cys382 and reconstituted into the phospholipid bilayers, the spin label partitions actively between hydrophobic and hydrophilic environments. In the DMPC bilayer, the hydrophobic component dominates, regardless of temperature. Mobility parameters (DeltaH(0)(-1)) are 0.3 and 0.73 G for the peptide in the DMPC or POPC bilayer environment, respectively. Interspin distances of doubly labeled hCB(1)(T377-E416) peptide reconstituted into a TFE/H(2)O mixture or a POPC or DMPC bilayer were estimated to be 10.6 +/- 0.5, 16.8 +/- 1, and 11.6 +/- 0.8 A, respectively. The extent of coupling (>or=50%) between spin labels located at i and i + 4 in a TFE/H(2)O mixture or a POPC bilayer is indicative of an alpha-helical TMH conformation, whereas the much lower coupling (14%) when the peptide is in a DMPC bilayer suggests a high degree of peptide conformational heterogeneity. These data demonstrate that hCB(1)(T377-E416) backbone dynamics as well as spin-label rotameric freedom are sensitive to and altered by the peptide's phospholipid bilayer environment, which exerts a dynamic influence on the conformation of a TMH critical to signal transmission by the hCB(1) receptor.

Significantly improved sensitivity of Q-band PELDOR/DEER experiments relative to X-band is observed in measuring the intercoil distance of a leucine zipper motif peptide (GCN4-LZ).

Pulsed electron double resonance (PELDOR)/double electron-electron resonance (DEER) spectroscopy is a very powerful structural biology tool in which the dipolar coupling between two unpaired electron spins (site-directed nitroxide spin-labels) is measured. These measurements are typically conducted at X-band (9.4 GHz) microwave excitation using the four-pulse DEER sequence and can often require up to 12 h of signal averaging for biological samples (depending on the spin-label concentration). In this work, we present for the first time a substantial increase in DEER sensitivity obtained by collecting DEER spectra at Q-band (34 GHz), when compared to X-band. The huge boost in sensitivity (factor of 13) demonstrated at Q-band represents a 169-fold decrease in data collection time, reveals a greatly improved frequency spectrum and higher-quality distance data, and significantly increases sample throughput. Thus, the availability of Q-band DEER spectroscopy should have a major impact on structural biology studies using site-directed spin labeling EPR techniques.

Molecular-scale force measurement in a coiled-coil peptide dimer by electron spin resonance.

A new method for measuring forces between small protein domains based on double electron-electron resonance (DEER) spectroscopy is demonstrated using a model peptide derived from the alpha-helical coiled-coil leucine zipper of yeast transcriptional activator GCN4. The equilibrium distribution of distances between two nitroxide spin labels rigidly attached to the helices of the dimer was determined by DEER and yielded a closing force of 100 +/- 10 pN between monomers, in excellent agreement with theoretical predictions.

Effect of sorbed methanol, current, and temperature on multicomponent transport in nafion-based direct methanol fuel cells.

The CO2 in the cathode exhaust of a liquid feed direct methanol fuel cell (DMFC) has two sources: methanol diffuses through the membrane electrode assembly (MEA) to the cathode where it is catalytically oxidized to CO2; additionally, a portion of the CO2 produced at the anode diffuses through the MEA to the cathode. The potential-dependent CO2 exhaust from the cathode was monitored by online electrochemical mass spectrometry (ECMS) with air and with H2 at the cathode. The precise determination of the crossover rates of methanol and CO2, enabled by the subtractive normalization of the methanol/air to the methanol/H2 ECMS data, shows that methanol decreases the membrane viscosity and thus increases the diffusion coefficients of sorbed membrane components. The crossover of CO2 initially increases linearly with the Faradaic oxidation of methanol, reaches a temperature-dependent maximum, and then decreases. The membrane viscosity progressively increases as methanol is electrochemically depleted from the anode/electrolyte interface. The crossover maximum occurs when the current dependence of the diffusion coefficients and membrane CO2 solubility dominate over the Faradaic production of CO2. The plasticizing effect of methanol is corroborated by measurements of the rotational diffusion of TEMPONE (2,2,6,6-tetramethyl-4-piperidone N-oxide) spin probe by electron spin resonance spectroscopy. A linear inverse relationship between the methanol crossover rate and current density confirms the absence of methanol electro-osmotic drag at concentrations relevant to operating DMFCs. The purely diffusive transport of methanol is explained in terms of current proton solvation and methanol-water incomplete mixing theories.

Electron spin resonance investigation of microscopic viscosity, ordering, and polarity in Nafion membranes containing methanol-water mixtures.

Electron spin resonance (ESR) was used to monitor the local environment of 2,2,6,6-tetramethyl-4-piperidone N-oxide (Tempone) spin probe in water and methanol mixtures in solution and in Li(+) ion exchanged Nafion 117 membranes. Solution spectra were analyzed using the standard fast-motion line width parameters, while membrane spectra were fitted using the microscopic order macroscopic disorder (MOMD) slow-motional line shape program of Freed and co-workers. The (14)N hyperfine splitting, aN, which reflects the local polarity of the nitroxide probe, decreases with increasing methanol concentration, consistent with the decrease in solvent polarity. The polarity depended only weakly on composition in the Nafion membrane, but was noticeably more temperature-dependent. The microviscosity of the membrane aqueous phase as reflected by the rotational correlation time (tauc) of the probe, was nearly 2 orders of magnitude longer in the membrane than in solution and varied by an order of magnitude over the composition range studied. The probe exhibits significant local ordering in the aqueous phase of Nafion membranes that is diminished with increasing methanol concentration.

Reversible pH-controlled DNA-binding peptide nanotweezers: an in-silico study.

We describe the molecular dynamics (MD)-aided engineering design of mutant peptides based on the alpha-helical coiled-coil GCN4 leucine zipper peptide (GCN4-p1) in order to obtain environmentally-responsive nanotweezers. The actuation mechanism of the nanotweezers depends on the modification of electrostatic charges on the residues along the length of the coiled coil. Modulating the solution pH between neutral and acidic values results in the reversible movement of helices toward and away from each other and creates a complete closed-open-closed transition cycle between the helices. Our results indicate that the mutants show a reversible opening of up to 15 A (1.5 nm; approximately 150% of the initial separation) upon pH actuation. Investigation on the physicochemical phenomena that influence conformational properties, structural stability, and reversibility of the coiled-coil peptide-based nanotweezers revealed that a rationale- and design-based approach is needed to engineer stable peptide or macromolecules into stimuli-responsive devices. The efficacy of the mutant that demonstrated the most significant reversible actuation for environmentally responsive modulation of DNA-binding activity was also demonstrated. Our results have significant implications in bioseparations and in the engineering of novel transcription factors.

Molecular modeling of chiral-modified zeolite HY employed in enantioselective separation.

Insight into enantioselective separation utilizing chiral-modified zeolite HY could be useful in designing a chiral stationary phase for resolving pharmaceutical compounds. A model was employed to better understand the enantioseparation of valinol in zeolite HY that contains (+)-(1R;2R)-hydrobenzoin as a chiral modifier. This model incorporates the zeolite support and accounts for the flexible change. Results from grand canonical Monte Carlo and molecular dynamics simulations indicate that the associated diastereomeric complex consists of a single (+)-(1R;2R)-hydrobenzoin and a single valinol molecules located in the zeolite HY supercage. Supercage-based docking simulation predicted an enantioselectivity of 2.6 compared with that of 1.4 measured experimentally. Also, the supercage-based docking simulation demonstrated a single binding motif in the S complex, and two binding motifs in the R complex. The multiple binding modes in the R complex resulted in its lower stability. This is hypothesized to be the origin of the weaker binding between (-)-(R)-valinol and the chiral modifier, and explains why (+)-(R)-valinol is retained more in the chiral-modified zeolite system studied.

Enantioseparation of phenylglycinol in chiral-modified zeolite HY: a molecular simulation study.

A mechanism has been proposed for the separation of valinol enantiomers using a chiral-modified zeolite HY (i.e., zeolite HY containing (+)-(1R;2R)-hydrobenzoin) Molecular modeling of chiral-modified zeolite HY employed in enantioselective separation. Jirapongphan SS, Warzywoda J, Budil DE, Sacco A Jr. Chirality 2007; in press, which accurately predicted the experimentally measured enantioseparation. This methodology has been applied to predict the separation of an enantiomeric pair of phenylglycinol molecules (a precursor in the synthesis of HIV-1 protease inhibitors) using the modified zeolite HY as a CSP. Phenylglycinol and valinol molecules are similar in terms of the presence of polar (i.e., amine and hydroxyl) groups. These functional groups are important in the proposed chiral discrimination. Supercage-based docking simulations yielded an enantioselectivity of 1.3 with (+)-(S)-phenylglycinol molecule better retained in the zeolite. Also, the simulations predicted two binding modes that were the same as those in the valinol system. This suggests that specific structural features (i.e., number and type of polar groups), which generate the hypothesized binding modes, are required in an enantioseparation utilizing the chiral-modified zeolite HY.

Calculating slow-motional electron paramagnetic resonance spectra from molecular dynamics using a diffusion operator approach.

A number of groups have utilized molecular dynamics (MD) to calculate slow-motional electron paramagnetic resonance (EPR) spectra of spin labels attached to biomolecules. Nearly all such calculations have been based on some variant of the trajectory method introduced by Robinson, Slutsky and Auteri (J. Chem. Phys. 1992,96, 2609-2616). Here we present an alternative approach that is specifically adapted to the diffusion operator-based stochastic Liouville equation (SLE) formalism that is also widely used to calculate slow-motional EPR line shapes. Specifically, the method utilizes MD trajectories to derive diffusion parameters such as the rotational diffusion tensor, diffusion tilt angles, and expansion coefficients of the orienting potential, which are then used as direct inputs to the SLE line shape program. This approach leads to a considerable improvement in computational efficiency over trajectory-based methods, particularly for high frequency, high field EPR. It also provides a basis for deconvoluting the effects of local spin label motion and overall motion of the labeled molecule or domain: once the local motion has been characterized by this approach, the label diffusion parameters may be used in conjunction with line shape analysis at lower EPR frequencies to characterize global motions. The method is validated by comparison of the MD predicted line shapes to experimental high frequency (250 GHz) EPR spectra.