How computational chemistry develops: a tribute to Peter Goodford.

This editorial discusses the foundation of aspects of computational chemistry and is a tribute to Peter Goodford, one of those founders, who recently passed away. Several colleagues describe Professor Goodford's work and the person himself.

Urgency and austerity as drivers of success.

This piece describes the approach by which even a small CADD (Computer-Aided Drug Design) group with limited resources and limited time can achieve substantial success given short budgets and the compressed, urgent environment of a biotech. Some comparisons are made with CADD operations in big pharma.

Biological Testing of Organophosphorus-Inactivated Acetylcholinesterase Oxime Reactivators Identified via Virtual Screening.

There is a pressing need for new therapeutics to reactivate covalently inactivated acetylcholinesterase (AChE) due to exposure to organophosphorus (OP) compounds. Current reactivation therapeutics (RTs) are not broad-spectrum and suffer from other liabilities, specifically the inability to cross the blood-brain-barrier. Additionally, the chemical diversity of available therapeutics is small, limiting opportunities for structure-activity relationship (SAR) studies to aid in the design of more effective compounds. In order to find new starting points for the development of oxime-containing therapeutic reactivators and to increase our base of knowledge, we have employed a combination of computational and experimental procedures to identify additional compounds with the real or potential ability to reactivate AChE while augmenting and complementing current knowledge. Computational methods were used to identify previously uninvestigated oxime-containing molecules. Experimentally, six compounds were found with reactivation capabilities comparable to, or exceeding, those of 2-pralidoxime (2-PAM) against a panel of AChE inactivated by paraoxon, diisopropylfluorophosphate (DFP), fenamiphos, and methamidophos. One compound showed enhanced reactivation ability against DFP and fenamiphos, the least tractable of these OPs to be reactivated.

Discovery and Development of LX7101, a Dual LIM-Kinase and ROCK Inhibitor for the Treatment of Glaucoma.

The structure of LX7101, a dual LIM-kinase and ROCK inhibitor for the treatment of ocular hypertension and associated glaucoma, is disclosed. Previously reported LIM kinase inhibitors suffered from poor aqueous stability due to solvolysis of the central urea. Replacement of the urea with a hindered amide resulted in aqueous stable compounds, and addition of solubilizing groups resulted in a set of compounds with good properties for topical dosing in the eye and good efficacy in a mouse model of ocular hypertension. LX7101 was selected as a clinical candidate from this group based on superior efficacy in lowering intraocular pressure and a good safety profile. LX7101 completed IND enabling studies and was tested in a Phase 1 clinical trial in glaucoma patients, where it showed efficacy in lowering intraocular pressure.

Exploring the physicochemical properties of oxime-reactivation therapeutics for cyclosarin, sarin, tabun, and VX inactivated acetylcholinesterase.

The inactivation of acetylcholinesterase (AChE) by organophosphorus agent (OP) compounds is a serious problem regardless of how the individual was exposed. The reactivation of OP-inactivated AChE is dependent on the OP conjugate, and commonly a specific oxime is better at reactivating a specific OP conjugate than several diverse OP conjugates. The presented research explores the physicochemical properties needed for the reactivation of OP-inactivated AChE. Four different OPs, cyclosarin, sarin, tabun, and VX, were analyzed using the same set of oxime reactivators. A trial descriptor pool of semiempirical, traditional, and molecular interaction field descriptors was used to construct an ensemble of QSAR models for each OP-conjugate pair. Based on the molecular information and the cross-validation ability, individual QSAR models were selected to be part of an OP-conjugate consensus model. The OP-conjugate specific models provide important insight into the physicochemical properties required to reactivate the OP conjugates of interest. The reactivation of AChE inactivated with either cyclosarin or tabun requires the oxime therapeutic to possess an overall polar-positive surface area. Oxime therapeutics for the reactivation of sarin-inactivated AChE are conformationally dependent while oxime reverse therapeutics for VX require a compact region with a highly hydrophilic region and two positively charged pyridine rings.

An atomic and molecular view of the depth dependence of the free energies of solute transfer from water into lipid bilayers.

Molecular interactions and orientations responsible for differences in 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) bilayer partitioning of three structurally related drug-like molecules (4-ethylphenol, phenethylamine, and tyramine) were investigated. This work is based on previously reported molecular dynamics (MD) simulations that determined their transverse free energy profiles across the bilayer. Previously, the location where the transfer free energy of the three solutes is highest, which defines the barrier domain for permeability, was found to be the bilayer center, while the interfacial region was found to be the preferred binding region. Contributions of the amino (NH2) and hydroxyl (OH) functional groups to the transfer free energies from water to the interfacial region were found to be very small both experimentally and by MD simulation, suggesting that the interfacial binding of these solutes is hydrophobically driven and occurs with minimal loss of hydrogen-bonding interactions of the polar functional groups which can occur with either water or phospholipid head groups. Therefore, interfacial binding is relatively insensitive to the number or type of polar functional groups on the solute. In contrast, the relative solute free energy in the barrier domain is highly sensitive to the number of polar functional groups on the molecule. The number and types of hydrogen bonds formed between the three solutes and polar phospholipid atoms or with water molecules were determined as a function of solute position in the bilayer. Minima were observed in the number of hydrogen bonds formed by each solute at the center of the bilayer, coinciding with a decrease in the number of water molecules in DOPC as a function of distance away from the interfacial region. In all regions, hydrogen bonds with water molecules account for the majority of hydrogen-bonding interactions observed for each solute. Significant orientational preferences for the solutes are evident in certain regions of the bilayer (e.g., within the ordered chain region and near the interfacial region 20-25 Å from the bilayer center). The preferred orientations are those that preserve favorable molecular interactions for each solute, which vary with the solute structure.

Functional group dependence of solute partitioning to various locations within a DOPC bilayer: a comparison of molecular dynamics simulations with experiment.

Atomic-level molecular dynamics simulations of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) bilayers containing small, amphiphilic, drug-like molecules were carried out to examine the influence of polar functionality on membrane partitioning and transport. Three related molecules (tyramine, phenethylamine, and 4-ethylphenol) were chosen to allow a detailed study of the isolated effects of the amine and hydroxyl functionalities on the preferred solute location, free energies of transfer, and the effect of combining both functional groups in a same molecule. Transfer free energy profiles (from water) generated from molecular dynamics (MD) simulations as a function of bilayer depth compared favorably to comparable experimental results. The simulations allowed the determination of the location of the barrier domain for permeability where the transfer free energy is highest and the preferred binding region at which the free energy is a minimum for each of the three solutes. Comparisons of the free energy profiles reveal that the hydrocarbon chain interior is the region most selective to chemical structure of different solutes because the free energies of transfer in that region vary to a significantly greater extent than in other regions of the bilayer. The contributions of the hydroxyl and amino groups to the free energies of solute transfer from water to the interfacial region were close to zero in both the MD simulations and experimental measurements. This suggests that the free energy decrease observed for solute transfer into the head group region occurs with minimal loss in solvation by hydrogen bonding to polar functional groups on the solute and is largely driven by hydrophobicity. Overall, the joint experimental and simulation studies suggest that the assumption of additivity of free energy contributions from multiple polar functional groups on the same molecule may hold for predictions of passive bilayer permeability coefficients providing that the groups are well isolated. However, this assumption does not hold for predictions of relative liposome-binding affinities.

Lead optimization and structure-based design of potent and bioavailable deoxycytidine kinase inhibitors.

A series of deoxycytidine kinase inhibitors was simultaneously optimized for potency and PK properties. A co-crystal structure then allowed merging this series with a high throughput screening hit to afford a highly potent, selective and orally bioavailable inhibitor, compound 10. This compound showed dose dependent inhibition of deoxycytidine kinase in vivo.

Substituent effects on the ionization and partitioning of p-(aminoethyl)phenols and structurally related compounds: electrostatic effects dependent on conformation.

Computational methods to predict pK(a) values and partition coefficients of drug molecules based on linear free energy relationships (LFERs) rely largely on the principles of independence and additivity of the functional group contributions in each molecule to the overall free energy. Nonadditivities in functional group contributions are often seen when multiple polar functional groups are in close proximity and in cases where conformational flexibility allows widely separated polar functional groups to interact. The degree to which long-range interactions may alter group contributions in more conformationally constrained molecules such as p-(aminoethyl)phenol and structurally similar analogs is more difficult to predict. In this study, both macroscopic and microscopic ionization constants and decadiene/water partition coefficients as a function of pH at 25 degrees C were obtained for p-(aminoethyl)phenol and six structurally related compounds to explore the reliability of the independence and additivity assumptions necessary in using the LFERs for predictions. A long-range interaction between the phenol and amine groups in the series has been found to affect the pK(a) values of both groups and to alter species-specific partition coefficients. Pronounced shifts in microscopic ionization constants involving zwitterion forms are clearly indicative of amplified long-range interactions between ionized substituents.

Potent and selective biphenyl azole inhibitors of adipocyte fatty acid binding protein (aFABP).

Herein we report the first disclosure of biphenyl azoles that are nanomolar binders of adipocyte fatty acid binding protein (aFABP or aP2) with up to thousand-fold selectivity against muscle fatty acid binding protein and epidermal fatty acid binding protein. In addition a new radio-ligand to determine binding against the three fatty acid binding proteins was also synthesized.

Human PEPT1 pharmacophore distinguishes between dipeptide transport and binding.

The human intestinal oligopeptide transporter (PEPT1) facilitates the absorption of dipeptides, tripeptides, and many peptidomimetic drugs. In this study, a large number of peptides were selected to investigate the structural features required for PEPT1 transport. Binding affinity was determined in a Gly-Sar uptake inhibition assay, whereas functional transport was ranked in a membrane depolarization assay. Although most of the peptides tested could bind to PEPT1, not all were substrates. As expected, single amino acids and tetrapeptides could not bind to or be transported by PEPT1. Dipeptide transport was influenced by charge, hydrophobicity, size, and side chain flexibility. The extent of transport was variable, and unexpectedly, some dipeptides were not substrates of PEPT1. These included dipeptides with two positive charges or extreme bulk in either position 1 or 2. Our results identify key features required for PEPT1 transport in contrast to most previously described pharmacophores, which are based on the inhibition of transport of a known substrate.

A novel high-throughput pepT1 transporter assay differentiates between substrates and antagonists.

PepT1 is a transporter of proven pharmaceutical utility for enhancing oral absorption. A high-throughput, robust functional assay, capable of distinguishing PepT1 binders from substrates, allowing identification and/or prediction of drug candidate activation was developed. An MDCK epithelial cell line was transfected with rPepT1. The high level of stable rPepT1 expression that was achieved enabled development of a miniaturized PepT1 assay in a 96-well format, which could be scaled to 384 wells. The assay is based on measurement of membrane depolarization resulting from the cotransport of protons and PepT1 substrates. Membrane potential changes are tracked with a voltage-sensitive fluorescent indicator. Control (mock-transfected) cells are used to determine nonspecific membrane potential changes. A variety of fluorescent dyes were tested during initial assay design, including intracellular pH and membrane potential indicators. A membrane potential indicator was chosen because of its superior performance. Upon PepT1 activation with glycylsarcosine, dose-dependent membrane depolarization was observed with an EC50 of 0.49 mM. Maximum depolarization was dependent on the level of PepT1 expression. Testing of 38 known PepT1 substrates, binders, and nonbinders demonstrated that this assay accurately distinguished substrates from binders and from nonbinders. Initial validation of this novel assay indicates that it is sensitive and robust, and can distinguish between transporter substrates and antagonists. This important distinction has been previously achieved only with lower-throughput assays. This assay might also be used to determine substrate potency and establish a high-quality data set for PepT1 SAR modeling.

In silico ADME/Tox: why models fail.

By way of example, we discuss the apparent 'failure' of in silico ADME/Tox models and attempt to understand the causes. Often, the interpretation of the success of models lies in their use and the expectations of the user. Other times, models are, in fact, of little value. Disappointing results can be linked to the key aspects of the model and modeling procedure, many of these related to the original data and its interpretation. We make recommendations to providers of models regarding the development, description, and use of models as well as the data and information that are important to understanding a model's quality and scope of use.

Analysis and optimization of structure-based virtual screening protocols. 2. Examination of docked ligand orientation sampling methodology: mapping a pharmacophore for success.

An important element of any structure-based virtual screening (SVS) technique is the method used to orient the ligands in the target active site. This has been a somewhat overlooked issue in recent SVS validation studies, with the assumption being made that the performance of an algorithm for a given set of orientation sampling settings will be representative for the general behavior of said technique. Here, we analyze five different SVS targets using a variety of sampling paradigms within the DOCK, GOLD and PROMETHEUS programs over a data set of approximately 10,000 noise compounds, combined with data sets containing multiple active compounds. These sets have been broken down by chemotype, with chemotype hit rate used to provide a measure of enrichment with a potentially improved relevance to real world SVS experiments. The variability in enrichment results produced by different sampling paradigms is illustrated, as is the utility of using pharmacophores to constrain sampling to regions that reflect known structural biology. The difference in results when comparing chemotype with compound hit rates is also highlighted.

Progress in understanding the structure-activity relationships of P-glycoprotein.

Efflux out of cells by P-glycoprotein (P-gp) represents a serious liability for pharmaceuticals, particularly for anti-cancer drugs. Consequently, identification of compounds as potential substrates is important for understanding their bioavailability. Also, the development of agents which reverse this multi-drug resistance phenotype has received considerable attention. Assays for determining these activities are reviewed. Recent literature and studies into the structure-activity relationships (SAR) of the resulting data are discussed. Multiple binding sites and other complicating factors have prevented the development of a truly general, conclusive SAR either for substrate or inhibitory activities. Consequently, many models have tended to address only very general properties, such as lipophilicity and size. However, progress has been made in the last few years toward more specific SAR suggesting well-defined structural features responsible for both activities. The future of understanding the details of P-gp SAR lies in more specific assays that target specific binding sites and mechanisms of action.