Surrogate data--a secure way to share corporate data

The privacy of chemical structure is of paramount importance for the industrial sector, in particular for the pharmaceutical industry. At the same time, companies handle large amounts of physico-chemical and biological data that could be shared in order to improve our molecular understanding of pharmacokinetic and toxicological properties, which could lead to improved predictivity and shorten the development time for drugs, in particular in the early phases of drug discovery. The current study provides some theoretical limits on the information required to produce reverse engineering of molecules from generated descriptors and demonstrates that the information content of molecules can be as low as less than one bit per atom. Thus theoretically just one descriptor can be used to completely disclose the molecular structure. Instead of sharing descriptors, we propose to share surrogate data. The sharing of surrogate data is nothing else but sharing of reliably predicted molecules. The use of surrogate data can provide the same information as the original set. We consider the practical application of this idea to predict lipophilicity of chemical compounds and we demonstrate that surrogate and real (original) data provides similar prediction ability. Thus, our proposed strategy makes it possible not only to share descriptors, but also complete collections of surrogate molecules without the danger of disclosing the underlying molecular structures.

Reverse engineering chemical structures from molecular descriptors: how many solutions?

Physical, chemical and biological properties are the ultimate information of interest for chemical compounds. Molecular descriptors that map structural information to activities and properties are obvious candidates for information sharing. In this paper, we consider the feasibility of using molecular descriptors to safely exchange chemical information in such a way that the original chemical structures cannot be reverse engineered. To investigate the safety of sharing such descriptors, we compute the degeneracy (the number of structure matching a descriptor value) of several 2D descriptors, and use various methods to search for and reverse engineer structures. We examine degeneracy in the entire chemical space taking descriptors values from the alkane isomer series and the PubChem database. We further use a stochastic search to retrieve structures matching specific topological index values. Finally, we investigate the safety of exchanging of fragmental descriptors using deterministic enumeration.

Molecular engineering of octupolar NLO molecules and materials based on bipyridyl metal complexes

Coordination compounds are of particular interest for the design of new chromophores with large nonlinear optical (NLO) susceptibilities. They offer a wide range of metals with different oxidation states and ligands, which can give rise to tunable electronic properties. Metal ions are excellent templates to build 2D and 3D octupolar NLO-phores. Their associations with functionalized bipyridyl ligands give rise to octahedral and tetrahedral metal complexes with large first-order hyperpolarizabilities. The ability to functionalize these octupoles allows their incorporation into macromolecular architectures such as polymers and metallodendrimers, We also show in this Account two approaches to induce noncentrosymmetry at the macroscopic level, either by supramolecular organization or by the all optical poling procedure.

Chemical engineering of the peptidyl transferase center reveals an important role of the 2'-hydroxyl group of A2451

The main enzymatic reaction of the large ribosomal subunit is peptide bond formation. Ribosome crystallography showed that A2451 of 23S rRNA makes the closest approach to the attacking amino group of aminoacyl-tRNA. Mutations of A2451 had relatively small effects on transpeptidation and failed to unequivocally identify the crucial functional group(s). Here, we employed an in vitro reconstitution system for chemical engineering the peptidyl transferase center by introducing non-natural nucleosides at position A2451. This allowed us to investigate the peptidyl transfer reaction performed by a ribosome that contained a modified nucleoside at the active site. The main finding is that ribosomes carrying a 2'-deoxyribose at A2451 showed a compromised peptidyl transferase activity. In variance, adenine base modifications and even the removal of the entire nucleobase at A2451 had only little impact on peptide bond formation, as long as the 2'-hydroxyl was present. This implicates a functional or structural role of the 2'-hydroxyl group at A2451 for transpeptidation.

Engineered lipids that cross-link the inner and outer leaflets of lipid bilayers

The application of supported lipid bilayer systems as molecular sensors, diagnostic devices, and medical implants is limited by their lack of stability. In an effort to enhance the stability of supported lipid bilayers, three pairs of phosphatidylcholine lipids were designed to cross-link at the termini of their 2-position acyl chain upon the formation of lipid bilayers. The cross-linked lipids span the lipid bilayer, resembling naturally occurring bolaamphiphiles that stabilize archaebacterial membranes against high temperatures. The three reactions investigated here include the acyl chain cross-linking between thiol and bromine groups, thiol and acryloyl groups, and cyclopentadiene and acryloyl groups. All three reactive lipid pairs were found to cross-link in liposomal membranes, as determined by thin-layer chromatography, ion-spray mass spectrometry, and 1H NMR. The monolayer film properties of the reactive amphiphiles were characterized by surface pressure-area isotherms and showed that stable monolayers formed at the air-water interface with limiting molecular areas comparable to that of pure saturated phosphatidylcholine lipids. Langmuir-Blodgett bilayers of dimyristoylphosphatidylcholine incorporating 15 mol % of the reactive thiol and acryloyl lipids had diffusion coefficients comparable with pure dimyristoylphosphatidylcholine, while bilayers with more than 25 mol % of the reactive lipids were immobile, suggesting that interleaflet cross-linking of the lipids inhibited membrane diffusion. Our results show that the reactive lipids can cross-link within a lipid bilayer and are suitable for assembling supported lipid bilayers using Langmuir-Blodgett deposition. By using terminally reactive amphiphiles to build up supported lipid bilayers with cross-linked leaflets, bolaamphiphiles can be incorporated into asymmetric solid supported membranes to increase their stability in biosensor and medical implant applications.

Structural Basis for Bile Acid Binding and Activation of the Nuclear Receptor FXR

The nuclear receptor FXR is the sensor of physiological levels of enterohepatic bile acids, the end products of cholesterol catabolism. Here we report crystal structures of the FXR ligand binding domain in complex with coactivator peptide and two different bile acids. An unusual A/B ring juncture, a feature associated with bile acids and no other steroids, provides ligand discrimination and triggers a pi-cation switch that activates FXR. Helix 12, the activation function 2 of the receptor, adopts the agonist conformation and stabilizes coactivator peptide binding. FXR is able to interact simultaneously with two coactivator motifs, providing a mechanism for enhanced binding of coactivators through intermolecular contacts between their LXXLL sequences. These FXR complexes provide direct insights into the design of therapeutic bile acids for treatment of hyperlipidemia and cholestasis.

Structure-property relationships of silicone biofouling-release coatings: effect of silicone network architecture on pseudobarnacle attachment strengths

Model silicone foul-release coatings with controlled molecular architecture were evaluated to determine the effect of compositional variables such as filler loading and crosslink density on pseudobarnacle attachment strength. Pseudobarnacle adhesion values correlated with filler loadings in both condensation and hydrosilylation-cured silicones. Variation of crosslink density of hydrosilylation-cured silicones had an insignificant effect on attachment strength. X-ray photoelectron spectroscopy (XPS) indicated that the mode of failure upon detachment of the pseudobarnacle was dependent upon the crosslink density; samples with high crosslink density failed cohesively within the silicone.

BioMOL: a computer-assisted biological modeling tool for complex chemical mixtures and biological processes at the molecular level

A chemical engineering approach for the rigorous construction, solution, and optimization of detailed kinetic models for biological processes is described. This modeling capability addresses the required technical components of detailed kinetic modeling, namely, the modeling of reactant structure and composition, the building of the reaction network, the organization of model parameters, the solution of the kinetic model, and the optimization of the model. Even though this modeling approach has enjoyed successful application in the petroleum industry, its application to biomedical research has just begun. We propose to expand the horizons on classic pharmacokinetics and physiologically based pharmacokinetics (PBPK), where human or animal bodies were often described by a few compartments, by integrating PBPK with reaction network modeling described in this article. If one draws a parallel between an oil refinery, where the application of this modeling approach has been very successful, and a human body, the individual processing units in the oil refinery may be considered equivalent to the vital organs of the human body. Even though the cell or organ may be much more complicated, the complex biochemical reaction networks in each organ may be similarly modeled and linked in much the same way as the modeling of the entire oil refinery through linkage of the individual processing units. The integrated chemical engineering software package described in this article, BioMOL, denotes the biological application of molecular-oriented lumping. BioMOL can build a detailed model in 1-1,000 CPU sec using standard desktop hardware. The models solve and optimize using standard and widely available hardware and software and can be presented in the context of a user-friendly interface. We believe this is an engineering tool with great promise in its application to complex biological reaction networks.

Crystal engineering of metalloporphyrin assemblies. New supramolecular architectures mediated by bipyridyl ligands

Targeted synthesis of new supramolecular motifs of metalloporphyrins in crystals by a concerted mechanism of molecular recognition in three dimensions, aided by organic ligands, is presented; it involves induced assembly of [tetrakis(4-hydroxyphenyl)porphyrinato]zinc species by a combination of axial coordination through bridging bipyridyls and of lateral hydrogen bonding.

Severity function describing the hydrolysis of xylan using carbonic acid

Beech wood derived xylan to hydrolyzed to predominantly xylose monomer units after exposure to hot, compressed liquid water saturated with carbon dioxide. Similar treatment without CO2 saturation resulted in only minor hydrolysis and a smaller fraction of monomers among the hydrolysis products. Severity of the hydrolysis reaction was correlated to reaction time, temperature, and carbon dioxide partial pressure and followed a function similar to those used to characterize mineral acid systems. Results from parallel hydrolysis experiments with an aqueous system and a very dilute sulfuric acid system allowed an approximation of the dissociation constant of carbonic acid in the temperature range of 170-230 degrees C. Results suggest that carbonic acid may be a viable reagent for promoting hydrolysis without mineral acids, especially in the case of a bioprocessing plant that produces carbon dioxide.

Cellulose hydrolysis under extremely low sulfuric acid and high-temperature conditions

The kinetics of cellulose hydrolysis under extremely low acid (ELA) conditions (0.07 wt%) and at temperatures >200 degrees C was investigated using batch reactors and bed-shrinking flow-through (BSFT) reactors. The maximum yield of glucose obtained from batch reactor experiments was about 60% for alpha-cellulose, which occurred at 205 and 220 degrees C. The maximum glucose yields from yellow poplar feedstocks were substantially lower, falling in the range of 26-50%. With yellow poplar feedstocks, a large amount of glucose was unaccounted for at the latter phase of the batch reactions. It appears that a substantial amount of released glucose condenses with nonglucosidic substances in liquid. The rate of glucan hydrolysis under ELA was relatively insensitive to temperature in batch experiments for all three substrates. This contradicts the traditional concept of cellulose hydrolysis and implies that additional factors influence the hydrolysis of glucan under ELA. In experiments using BSFT reactors, the glucose yields of 87.5, 90.3, and 90.8% were obtained for yellow poplar feedstocks at 205, 220, and 235 degrees C, respectively. The hydrolysis rate for glucan was about three times higher with the BSFT than with the batch reactors. The difference of observed kinetics and performance data between the BSFT and the batch reactors was far above that predicted by the reactor theory.

Measurement of bubble size distribution in protein foam fractionation column using capillary probe with photoelectric sensors

Bubble size is a key variable for predicting the ability to separate and concentrate proteins in a foam fractionation process. It is used to characterize not only the bubble-specific interfacial area but also coalescence of bubbles in the foam phase. This article describes the development of a photoelectric method for measuring the bubble size distribution in both bubble and foam columns for concentrating proteins. The method uses a vacuum to withdraw a stream of gas-liquid dispersion from the bubble or foam column through a capillary tube with a funnel-shaped inlet. The resulting sample bubble cylinders are detected, and their lengths are calculated by using two pairs of infrared photoelectric sensors that are connected with a high-speed data acquisition system controlled by a microcomputer. The bubble size distributions in the bubble column 12 and 1 cm below the interface and in the foam phase 1 cm above the interface are obtained in a continuous foam fractionation process for concentrating ovalbumin. The effects of certain operating conditions such as the feed protein concentration, superficial gas velocity, liquid flow rate, and solution pH are investigated. The results may prove to be helpful in understanding the mechanisms controlling the foam fractionation of proteins.

Neutrality condition and response law for nonlinear reaction-diffusion equations, with application to population genetics

We study a general class of nonlinear macroscopic evolution equations with "transport" and "reaction" terms which describe the dynamics of a species of moving individuals (atoms, molecules, quasiparticles, organisms, etc.). We consider that two types of individuals exist, "not marked" and "marked," respectively. We assume that the concentrations of both types of individuals are measurable and that they obey a neutrality condition, that is, the kinetic and transport properties of the "not marked" and "marked" individuals are identical. We suggest a response experiment, which consists in varying the fraction of "marked" individuals with the preservation of total fluxes, and show that the response of the system can be represented by a linear superposition law even though the underlying dynamics of the system is in general highly nonlinear. The linear response law is valid even for large perturbations and is not the result of a linearization procedure but rather a necessary consequence of the neutrality condition. First, we apply the response theorem to chemical kinetics, where the "marked species" is a molecule labeled with a radioactive isotope and there is no kinetic isotope effect. The susceptibility function of the response law can be related to the reaction mechanism of the process. Secondly we study the geographical distribution of the nonrecurrent, nonreversible neutral mutations of the nonrecombining portion of the Y chromosome from human populations and show that the fraction of mutants at a given point in space and time obeys a linear response law of the type introduced in this paper. The theory may be used for evaluating the geographic position and the moment in time where and when a mutation originated.

Engineered allosteric ribozymes as biosensor components

RNA and DNA molecules can be engineered to function as molecular switches that trigger catalytic events when a specific target molecule becomes bound. Recent studies on the underlying biochemical properties of these constructs indicate that a significant untapped potential exists for the practical application of allosteric nucleic acids. Engineered molecular switches can be used to report the presence of specific analytes in complex mixtures, making possible the creation of new types of biosensor devices and genetic control elements.

Purification of non-toxic, biodegradable arginine-based gemini surfactants, bis(Args), by ion exchange chromatography

This paper presents an environmentally improved procedure for the preparative purification of a series of arginine-based gemini surfactants. The technique used was cation-exchange chromatography. Mixtures of boric-borate buffer, co-solvent (ethanol), and sodium chloride were tested as eluents. The influence of the buffer pH and the amount of co-solvent on the chromatographic process was studied for the model compound bis(Nalpha-lauroyl-L-arginine) 1,3-propanediamide dihydrochloride, C3(LA)2, and purification conditions were established. The method was scaled-up to the multigram level for C3(LA)2 and the rest of the series. The proposed preparative procedure involves simple equipment, low cost materials, and minimal amounts of solvent (water/ethanol), with low toxicity.

Production of microbial polyester by fermentation of recombinant microorganisms

Polyhydroxyalkanoates (PHAs) can be produced from renewable sources and are biodegradable with similar material properties and processibility to conventional plastic materials. With recent advances in our understanding of the biochemistry and genetics of PHA biosynthesis and cloning of the PHA biosynthesis genes from a number of different bacteria, many different recombinant bacteria have been developed to improve PHA production for commercial applications. For enhancing PHA synthetic capacity, homologous or heterologous expression of the PHA biosynthetic enzymes has been attempted. Several genes that allow utilization of various substrates were transformed into PHA producers, or non-PHA producers utilizing inexpensive carbon substrate were transformed with the PHA biosynthesis genes. Novel PHAs have been synthesized by introducing a new PHA biosynthesis pathway or a new PHA synthase gene. In this article, recent advances in the production of PHA by recombinant bacteria are described.

Oxidative lime pretreatment of high-lignin biomass: poplar wood and newspaper

Lime (Ca[OH]2) and oxygen (O2) were used to enhance the enzymatic digestibility of two kinds of high-lignin biomass: poplar wood and newspaper. The recommended pretreatment conditions for poplar wood are 150 degrees C, 6 h, 0.1 g of Ca(OH)2/g of dry biomass, 9 mL of water/g of dry biomass, 14.0 bar absolute oxygen, and a particle size of -10 mesh. Under these conditions, the 3-d reducing sugar yield of poplar wood using a cellulase loading of 5 filter paper units (FPU)/g of raw dry biomass increased from 62 to 565 mg of eq. glucose/g of raw dry biomass, and the 3-d total sugar (glucose + xylose) conversion increased from 6 to 77% of raw total sugars. At high cellulase loadings (e.g., 75 FPU/g of raw dry biomass), the 3-d total sugar conversion reached 97%. In a trial run with newspaper, using conditions of 140 degrees C, 3 h, 0.3 g of Ca(OH)2/g of dry biomass, 16 mL of water/g of dry biomass, and 7.1 bar absolute oxygen, the 3-d reducing sugar yield using a cellulase loading of 5 FPU/g of raw dry biomass increased from 240 to 565 mg of eq. glucose/g of raw dry biomass. A material balance study on poplar wood shows that oxidative lime pretreatment solubilized 38% of total biomass, including 78% of lignin and 49% of xylan; no glucan was removed. Ash increased because calcium was incorporated into biomass during the pretreatment. After oxidative lime pretreatment, about 21% of added lime could be recovered by CO2 carbonation.