Biomedical subjects

Alexander M Klibanov

Publications and source records attributed to Alexander M Klibanov.

At least 19 recordsLinked to original sources

PubMed2006

Why inhaling salt water changes what we exhale.

We find that inhaling salt water diminishes subsequently exhaled biomaterial in man and animals due to reversible stabilization of the airway lining fluid (ALF)/air interface as a novel potential means for control of the spread of airborne infectious disease. The mechanism of this phenomenon relates to charge shielding of mucin or mucin-like macromolecules that consequently undergo gelation; this gelation alters the physical properties of the ALF surface and reduces its breakup. Cations in the nebulized solution and apparent surface viscoelasticity of the ALF (more than any other ALF intrinsic physical property) appear to be responsible for the reduced tendency of the ALF to disintegrate into very small droplets. We confirm these effects in vivo and show their reversibility through nebulization of saline solutions to anesthetized bull calves.

Administration, Inhalation↗

PubMed2006

Polymeric coatings that inactivate both influenza virus and pathogenic bacteria.

Painting a glass slide with branched or linear N,N-dodecyl methyl-polyethylenimines (PEIs) and certain other hydrophobic PEI derivatives enables it to kill influenza virus with essentially a 100% efficiency (at least a 4-log reduction in the viral titer) within minutes, as well as the airborne human pathogenic bacteria Escherichia coli and Staphylococcus aureus. For most of the coating polyions, this virucidal action is shown to be on contact, i.e., solely by the polymeric chains anchored to the slide surface; for others, a contribution of the polyion leaching from the painted surface cannot be ruled out. A relationship between the structure of the derivatized PEI and the resultant virucidal activity of the painted surface has been elucidated.

Animals↗

PubMed2006

Specificity of a DNA-based (DNAzyme) peroxidative biocatalyst.

A complex formation between hemin and a congruous oligonucleotide not only greatly enhances the former's peroxidative activity but also results in a biocatalyst (DNAzyme) with a novel specificity. Herein substrate, regio-, enantiomeric, and diastereomeric selectivities of heme, the DNAzyme, and the enzyme horseradish peroxidase are comparatively examined.

Catalysis↗

PubMed2006

Moisture-induced aggregation of lyophilized DNA and its prevention.

PURPOSE: To investigate the moisture-induced aggregation (i.e., a loss of solubility in water) of DNA in a solid state and to develop rational strategies for its prevention. METHODS: Lyophilized calf thymus DNA was exposed to relative humidity (RH) levels from 11% to 96% at 55 degrees C. Following a 24-h incubation under these stressed conditions, the solubility of DNA in different aqueous solutions and the water uptake of DNA were determined. The effects of solution pH and NaCl concentration and the presence of excipients (dextran and sucrose) on the subsequent moisture-induced aggregation of DNA were examined. The extent of this aggregation was compared with that of a supercoiled plasmid DNA. RESULTS: Upon a 24-h incubation at 55 degrees C, calf thymus DNA underwent a major moisture-induced aggregation reaching a maximum at a 60% RH; in contrast, the single-stranded DNA exhibited the maximal aggregation at a 96% RH. Moisture uptake and aqueous solubility studies revealed that the aggregation was primarily due to formation of inter-strand hydrogen bonds. Aggregation of DNA also proceeded at 37 degrees C, albeit at a slower rate. Solution pH and NaCl concentration affected DNA aggregation only at higher RH levels. This aggregation was markedly reduced by co-lyophilization with dextran or sucrose (but not with PEG). The aggregation pattern of a supercoiled plasmid DNA was similar to that of its linear calf thymus counterpart. CONCLUSIONS: The moisture-induced aggregation of lyophilized DNA is caused mainly by non-covalent cross-links between disordered, single-stranded regions of DNA. At high RH levels, renaturation and aggregation of DNA compete with each other. The aggregation is minimized at low RH levels, at optimal solution pH and salt concentration prior to lyophilization, and by co-lyophilizing with excipients capable of forming multiple hydrogen bonds, e.g., dextran and sucrose.

Animals↗

PubMed2006

Co-lyophilization with D-proline greatly enhances peroxidase's stereoselectivity in a non-aqueous medium.

The impact of co-lyophilizing horseradish peroxidase (HRP) with numerous amino acids and other chiral excipients on the enzyme's subsequent stereoselectivity [E(S/R)] in the sulfoxidation of thioanisole in 2-propanol was systematically investigated. While many improved the stereoselectivity of (and significantly activated) HRP, the greatest effect was observed with D-proline which enhanced the E(S/R) value by over an order of magnitude from synthetically meaningless to useful.

2-Propanol↗

PubMed2005

Sequence optimization and designability of enzyme active sites.

We recently found that many residues in enzyme active sites can be computationally predicted by the optimization of scoring functions based on substrate binding affinity, subject to constraints on the geometry of catalytic residues and protein stability. Here, we explore the generality of this surprising observation. First, the impact of hydrogen-bonding networks necessary for catalysis on the accuracy of sequence optimization is assessed; incorporation of these networks, where relevant, into the set of catalytic constraints is found to be essential. Next, the impact of multiple substrate selectivity on sequence optimization is probed by carrying out independent calculations for complexes of deoxyribonucleoside kinases with various cognate ligands, revealing how simultaneous selection pressures determined active-site sequences of these enzymes. Including previous calculations on simpler enzymes, computational sequence optimization correctly predicts 76% of all active-site residues tested (86% correct, with 93% similar, for naturally conserved residues). In these studies, the ligand is fixed in its native conformation. To assess the applicability of these methods to de novo active-site design, the effect of small ligand motions around the native pose is also examined. Robustness of sequence accuracy for topologically similar poses is demonstrated for selected kinases, but not for a model peptidase. Based on these observations, we introduce the notion of the designability of an enzyme active site, a metric that may be used to guide the search for protein scaffolds suitable for the introduction of de novo activity for a desired chemical reaction.

Algorithms↗

PubMed2005

Computational prediction of native protein ligand-binding and enzyme active site sequences.

Recent studies reveal that the core sequences of many proteins were nearly optimized for stability by natural evolution. Surface residues, by contrast, are not so optimized, presumably because protein function is mediated through surface interactions with other molecules. Here, we sought to determine the extent to which the sequences of protein ligand-binding and enzyme active sites could be predicted by optimization of scoring functions based on protein ligand-binding affinity rather than structural stability. Optimization of binding affinity under constraints on the folding free energy correctly predicted 83% of amino acid residues (94% similar) in the binding sites of two model receptor-ligand complexes, streptavidin-biotin and glucose-binding protein. To explore the applicability of this methodology to enzymes, we applied an identical algorithm to the active sites of diverse enzymes from the peptidase, beta-gal, and nucleotide synthase families. Although simple optimization of binding affinity reproduced the sequences of some enzyme active sites with high precision, imposition of additional, geometric constraints on side-chain conformations based on the catalytic mechanism was required in other cases. With these modifications, our sequence optimization algorithm correctly predicted 78% of residues from all of the enzymes, with 83% similar to native (90% correct, with 95% similar, excluding residues with high variability in multiple sequence alignments). Furthermore, the conformations of the selected side chains were often correctly predicted within crystallographic error. These findings suggest that simple selection pressures may have played a predominant role in determining the sequences of ligand-binding and active sites in proteins.

Algorithms↗

PubMed2005

Immobilized N-alkylated polyethylenimine avidly kills bacteria by rupturing cell membranes with no resistance developed.

Several critical mechanistic and phenomenological aspects of the microbicidal surface coatings based on immobilized hydrophobic polycations, previously developed by us, are addressed. Using Escherichia coli (Gram-negative) and Staphylococcus aureus (Gram-positive) bacteria, remarkable bactericidal action (up to a 10(9)-fold reduction in live bacteria count in the surface-exposed solution and a 100% inactivation of the surface-adhered bacteria) of an amino-glass slide covalently derivatized with N-hexyl,methyl-polyethylenimine (PEI) is found to be due to rupturing bacterial cell membranes by the polymeric chains. The bacteria fail to develop noticeable resistance to this lethal action over the course of many successive generations. Finally, the immobilized N-alkyl-PEI, while deadly to bacteria, is determined to be harmless to mammalian (monkey kidney) cells.

Animals↗

PubMed2005

Mechanistic studies on aggregation of polyethylenimine-DNA complexes and its prevention.

Aggregation of polyethylenimine (PEI)-DNA complexes severely undermines their utility for gene delivery into mammalian cells. Herein we undertook to elucidate the mechanism of this deleterious phenomenon and to develop rational strategies for its prevention. The effect of temperature, surfactants, complex concentration, ionic strength, viscosity, and pH on the time course of this aggregation was systematically examined. The aggregation process was completely inhibited by 2.5% polyoxyethylene (100) stearate (POES) and to a lesser degree by other nonionic surfactants. Importantly, POES preserved the transfection efficiency of the complexes without inducing toxicity. The aggregation was also reduced by lowering the temperature and pH, diluting the complexes, and increasing the solution viscosity. It is concluded that PEI-DNA complexes aggregate primarily due to hydrophobic interactions, while electrostatic attractions play little role.

Animals↗

PubMed2005

Full deacylation of polyethylenimine dramatically boosts its gene delivery efficiency and specificity to mouse lung.

High-molecular-mass polyethylenimines (PEIs) are widely used vectors for nucleic acid delivery. We found that removal of the residual N-acyl moieties from commercial linear 25-kDa PEI enhanced its plasmid DNA delivery efficiency 21 times in vitro, as well as 10,000 times in mice with a concomitant 1,500-fold enhancement in lung specificity. Several additional linear PEIs were synthesized by acid-catalyzed hydrolysis of poly(2-ethyl-2-oxazoline), yielding the pure polycations. PEI87 and PEI217 exhibited the highest efficiency in vitro: 115-fold and 6-fold above those of the commercial and deacylated PEI25s, respectively; moreover, PEI87 delivered DNA to mouse lung as efficiently as the pure PEI25 but at a lower concentration and with a 200-fold lung specificity. These improvements stem from an increase in the number of protonatable nitrogens, which presumably results in a tighter condensation of plasmid DNA and a better endosomal escape of the PEI/DNA complexes. As a validation of the potential of such linear, fully deacylated PEIs in gene therapy for lung diseases, systemic delivery in mice of the complexes of a short interfering RNA (siRNA) against a model gene, firefly luciferase, and PEI25 or PEI87 afforded a 77% and 93% suppression of the gene expression in the lungs, respectively. Furthermore, a polyplex of a siRNA against the influenza viral nucleocapsid protein gene and PEI87 resulted in a 94% drop of virus titers in the lungs of influenza-infected animals.

Acylation↗

PubMed2005

Exploring polyethylenimine-mediated DNA transfection and the proton sponge hypothesis.

BACKGROUND: The relatively high transfection efficiency of polyethylenimine (PEI) vectors has been hypothesized to be due to their ability to avoid trafficking to degradative lysosomes. According to the proton sponge hypothesis, the buffering capacity of PEI leads to osmotic swelling and rupture of endosomes, resulting in the release of the vector into the cytoplasm. METHODS: The mechanism of PEI-mediated DNA transfer was investigated using quantitative methods to study individual steps in the overall transfection process. In addition to transfection efficiency, the cellular uptake, local pH environment, and stability of vectors were analyzed. N-Quaternized (and therefore non-proton sponge) versions of PEI and specific cell function inhibitors were used to further probe the proton sponge hypothesis. RESULTS: Both N-quaternization and the use of bafilomycin A1 (a vacuolar proton pump inhibitor) reduced the transfection efficiency of PEI by approximately two orders of magnitude. Chloroquine, which buffers lysosomes, enhanced the transfection efficiency of N-quaternized PEIs and polylysine by 2-3-fold. In contrast, chloroquine did not improve the transfection efficiency of PEI. The measured average pH environment of PEI vectors was 6.1, indicating that they successfully avoid trafficking to acidic lysosomes. Significantly lower average pH environments were observed for permethyl-PEI (pH 5.4), perethyl-PEI (pH 5.1), and polylysine (pH 4.6) vectors. Cellular uptake levels of permethyl-PEI and perethyl-PEI vectors were found to be 20 and 90% higher, respectively, than that of parent PEI vectors, indicating that the reduction in transfection activity of the N-quaternized PEIs is due to a barrier downstream of cellular uptake. A polycation/DNA-binding affinity assessment showed that the more charge dense N-quaternized PEIs bind DNA less tightly than PEI, demonstrating that poor vector unpackaging was not responsible for the reduced transfection activity of the N-quaternized PEIs. CONCLUSIONS: The results obtained are consistent with the proton sponge hypothesis and strongly suggest that the transfection activity of PEI vectors is due to their unique ability to avoid acidic lysosomes.

Animals↗

PubMed2005

Cross-linked small polyethylenimines: while still nontoxic, deliver DNA efficiently to mammalian cells in vitro and in vivo.

PURPOSE: Polyethylenimine (PEI) is among the most efficient nonviral gene delivery vectors. Its efficiency and cytotoxicity depend on molecular weight, with the 25-kDa PEI being most efficient but cytotoxic. Smaller PEIs are noncytotoxic but less efficient. Enhancement in gene delivery efficiency with minimal cytotoxicity by cross-linking of small PEIs via potentially biodegradable linkages was explored herein. The hypothesis was that cross-linking would raise the polycation's effective molecular weight and hence the transfection efficiency, while biodegradable linkages would undergo the intracellular breakdown after DNA delivery and hence not lead to cytotoxicity. Toward this goal, we carried out cross-linking of branched 2-kDa PEI and its 1:1 (w/w) mixture with a linear 423-Da PEI via ester- and/or amide-bearing linkages; the in vitro and in vivo gene delivery efficiency, as well as toxicity to mammalian cells, of the resultant cross-linked polycations were investigated. METHODS: The efficiency of the cross-linked PEIs in delivering in vitro a plasmid containing beta-galactosidase gene and their cytotoxicity were investigated in monkey kidney cells (COS-7). Dynamic light scattering was used to compare the relative DNA condensation efficiency of the unmodified and cross-linked PEIs. In vivo gene delivery efficiency was evaluated by intratracheal delivery in mice of the complexes of a luciferase-encoding plasmid and the PEIs and estimating the luciferase expression in the lungs. RESULTS: Cross-linking boosted the gene delivery efficiency of the small PEIs by 40- to 550-fold in vitro; the efficiency of the most potent conjugates even exceeded by an order of magnitude that of the branched 25-kDa PEI. Effective condensation of DNA was evident from the fact that the mean diameter of the complexes of the cross-linked PEIs was some 300 nm with a narrow size distribution, while the complexes of the unmodified small PEIs exhibited a mean size of >700 nm with a very broad size distribution. At concentrations where the 25-kDa PEI resulted in >95% cell death, the conjugates afforded nearly full cell viability. The cross-linked PEIs were 17 to 80 times more efficient than the unmodified ones in vivo; furthermore, their efficiencies were up to twice that of the 25-kDa PEI. CONCLUSIONS: Cross-linking of small PEIs with judiciously designed amide- and ester-bearing linkers boosts their gene delivery efficiency both in vitro and in vivo without increasing the cytotoxicity. The high efficiency is dependent on the nature of the linkages and the PEIs used.

Animals↗

PubMed2005

Surpassing nature: rational design of sterile-surface materials.

The rise of multidrug-resistant pathogens and recalcitrance of biofilm infections present a formidable challenge to combating infectious diseases. There are numerous disinfectants and antiseptics for treating materials in hospitals and community settings, and devices such as catheters impregnated with anti-infectives have been introduced into practice. However, there are many limitations of materials impregnated with a leaching antibacterial agent. Recently, non-leaching, permanent, sterile-surface materials have been developed in which one end of a long-chained hydrophobic polycation containing antimicrobial monomers is attached covalently to the surface of a material, for example, cotton or plastic. The polymeric chain allows the antimicrobial moieties to permeate into, and kill, the cells of the pathogen. These sterile-surface materials kill both air- and waterborne pathogens and are not susceptible to existing resistance mechanisms.

Biomedical Engineering↗

PubMed2005

Polycation-mediated delivery of siRNAs for prophylaxis and treatment of influenza virus infection.

Influenza A virus causes one of the most prevalent infections in humans. In a typical year, 10-20% of the population of the US is infected by influenza virus, resulting in up to 40,000 deaths and 200,000 hospitalisations. Vaccination is the most effective preventative measure that can protect 70-90% of healthy adults aged < 65; however, the protection rate is much lower in those most susceptible to infection, namely infants, the elderly and individuals with weakened immune systems. Although four drugs have been approved by the FDA for use as prophylaxis and/or treatment of influenza, concerns about their side effects and the emergence of drug-resistant viruses persist. RNA interference (RNAi), an emerging method of post transcriptional gene silencing, appears ideal for the prevention and treatment of influenza. RNAi in mammals can be mediated by short interfering RNAs (siRNAs) of approximately 21-27 nucleotides in length. The authors have previously shown that siRNAs specific for conserved regions of the influenza virus genome are potent inhibitors of influenza virus replication in both cell lines and chicken embryos. This review discusses the recent progress in the in vivo inhibition of influenza virus by the delivery of siRNAs mediated by non-viral vectors, and the prospects of this strategy for prophylaxis and treatment of influenza infection in humans.

Animals↗

PubMed2004

Drastically lowering the titer of waterborne bacteriophage PRD1 by exposure to immobilized hydrophobic polycations.

Decrease in the titer of bacteriophage PRD1 (a model of animal adenoviruses) in aqueous solutions caused by the presence of systematically chemically derivatized surfaces was kinetically investigated. The greatest loss of infectivity--up to a 4-log reduction in the titer--was observed with immobilized hydrophobic polyethylenimine-based and dendrimer-based polycations.

Adsorption↗

PubMed2004

On the relationship between conformation and stability in solid pharmaceutical protein formulations.

Long-term stability is critical in the successful development of pharmaceuticals, including macromolecular ones, such as proteins. Due to the relative instability of aqueous solutions of proteins, they are typically stores in a freeze-dried (lyophilized) state. However, proteins reversibly (and sometimes even irreversibly) denature upon lyophilization and consequently adopt conformations markedly distinct from the native ones. This phenomenon may profoundly affect deleterious processes in lyophilized proteins, e.g. moisture-induced aggregation, as illustrated in this review with bovine serum and recombinant human albumins.

Albumins↗

PubMed2003

Nanocrystals modified with peptide nucleic acids (PNAs) for selective self-assembly and DNA detection.

Gold nanocrystals modified with peptide nucleic acids (PNAs) have been prepared and applied to self-assembly and DNA sensing. Experiments with different PNA structural motifs show that (1). the versatility in PNA synthetic design can be used to modulate the electrostatic surface properties of nanocrystals, presenting an opportunity to control assembly rate and aggregate size, (2). short (6 base) PNAs can hybridize effectively while attached to nanoparticles, providing a route to generating materials with small interparticle spacings, and (3). the superior base pair mismatch selectivity of PNAs is further enhanced on nanosurfaces, enabling PNA-modified nanoparticles to act as highly selective nanoscale sensors, as well as synthons for defect-free self-assembly. This last feature was coupled with a substantial change in colloidal stability upon DNA hybridization to develop a novel colorimetric DNA assay that detects the presence of single base imperfections within minutes. Various modes of PNA hybridization, including the first practical application of PNA-PNA interactions, were used to direct the assembly of nanoparticles into macroscopic arrangements. Shorter duplex interconnects and greater specificity in assembly were obtained compared to similar experiments with DNA-modified nanocrystals.

Base Pair Mismatch↗

PubMed2003

Conjugation to gold nanoparticles enhances polyethylenimine's transfer of plasmid DNA into mammalian cells.

Branched polyethylenimine (PEI) chains with an average molecular mass of 2 kDa (PEI2) have been covalently attached to gold nanoparticles (GNPs), and the potency of the resulting PEI2-GNPs conjugates as vectors for the delivery of plasmid DNA into monkey kidney (COS-7) cells in the presence of serum in vitro has been systematically investigated. The transfection efficiencies vary as a function of the PEI/gold molar ratio in the conjugates, with the best one (PEI2-GNPII) being 12 times more potent than the unmodified polycation. This potency can be further doubled by adding amphiphilic N-dodecyl-PEI2 during complex formation with DNA. The resulting ternary complexes are at least 1 order of magnitude more efficient than the 25-kDa PEI, one of the premier polycationic gene-delivery vectors. Importantly, although unmodified PEI2 transfects just 4% of the cells, PEI2-GNPII transfects 25%, and the PEI2-GNPII/dodecyl-PEI2 ternary complex transfects 50% of the cells. The intracellular trafficking of the DNA complexes of these vectors, monitored by transmission electron microscopy, has detected the complexes in the nucleus <1 h after transfection.

Animals↗