Enoch S. Huang

Physiochemical drug properties associated with in vivo toxicological outcomes

Relationships between physicochemical drug properties and toxicity were inferred from a data set consisting of animal in vivo toleration (IVT) studies on 245 preclinical Pfizer compounds; an increased likelihood of toxic events was found for less polar, more lipophilic compounds. This trend held across a wide range of types of toxicity and across a broad swath of chemical space.

Structure-based maximal affinity model predicts small-molecule druggability

Lead generation is a major hurdle in small-molecule drug discovery, with an estimated 60% of projects failing from lack of lead matter or difficulty in optimizing leads for drug-like properties. It would be valuable to identify these less-druggable targets before incurring substantial expenditure and effort. Here we show that a model-based approach using basic biophysical principles yields good prediction of druggability based solely on the crystal structure of the target binding site. We quantitatively estimate the maximal affinity achievable by a drug-like molecule, and we show that these calculated values correlate with drug discovery outcomes. We experimentally test two predictions using high-throughput screening of a diverse compound collection. The collective results highlight the utility of our approach as well as strategies for tackling difficult targets.

Are protein–protein interfaces more conserved in sequence than the rest of the protein surface?

Protein interfaces are thought to be distinguishable from the rest of the protein surface by their greater degree of residue conservation. We test the validity of this approach on an expanded set of 64 protein–protein interfaces using conservation scores derived from two multiple sequence alignment types, one of close homologs/orthologs and one of diverse homologs/paralogs. Overall, we find that the interface is slightly more conserved than the rest of the protein surface when using either alignment type, with alignments of diverse homologs showing marginally better discrimination. However, using a novel surface‐patch definition, we find that the interface is rarely significantly more conserved than other surface patches when using either alignment type. When an interface is among the most conserved surface patches, it tends to be part of an enzyme active site. The most conserved surface patch overlaps with 39% (± 28%) and 36% (± 28%) of the actual interface for diverse and close homologs, respectively. Contrary to results obtained from smaller data sets, this work indicates that residue conservation is rarely sufficient for complete and accurate prediction of protein interfaces. Finally, we find that obligate interfaces differ from transient interfaces in that the former have significantly fewer alignment gaps at the interface than the rest of the protein surface, as well as having buried interface residues that are more conserved than partially buried interface residues.

AB INITIO PROTEIN STRUCTURE PREDICTION USING A COMBINED HIERARCHICAL APPROACH

As part of the third Critical Assessment of Structure Prediction meeting (CASP3), we predict the three‐dimensional structures for 13 proteins using a hierarchical approach. First, all possible compact conformations of a protein sequence are enumerated using a highly simplified tetrahedral lattice model. We select a large subset of these conformations using a lattice‐based scoring function and build detailed all‐atom models incorporating predicted secondary structure. A combined all‐atom knowledge‐based scoring function is then used to select three smaller subsets from these all‐atom models. Finally, a consensus‐based distance geometry procedure is used to generate the best conformations from each of the all‐atom subsets. With this method, we are able to predict the global topology/shape for all or a large part of the sequence for six out of the thirteen proteins. For two other proteins, the topology/shape for shorter fragments are predicted. This represents a marked improvement in ab initio prediction since CASP was first instigated in 1994. Proteins Suppl 1999;3:194–198.

Causal reasoning on biological networks

MOTIVATION The interpretation of high-throughput datasets has remained one of the central challenges of computational biology over the past decade. Furthermore, as the amount of biological knowledge increases, it becomes more and more difficult to integrate this large body of knowledge in a meaningful manner. In this article, we propose a particular solution to both of these challenges. METHODS We integrate available biological knowledge by constructing a network of molecular interactions of a specific kind: causal interactions. The resulting causal graph can be queried to suggest molecular hypotheses that explain the variations observed in a high-throughput gene expression experiment. We show that a simple scoring function can discriminate between a large number of competing molecular hypotheses about the upstream cause of the changes observed in a gene expression profile. We then develop an analytical method for computing the statistical significance of each score. This analytical method also helps assess the effects of random or adversarial noise on the predictive power of our model. RESULTS Our results show that the causal graph we constructed from known biological literature is extremely robust to random noise and to missing or spurious information. We demonstrate the power of our causal reasoning model on two specific examples, one from a cancer dataset and the other from a cardiac hypertrophy experiment. We conclude that causal reasoning models provide a valuable addition to the biologists toolkit for the interpretation of gene expression data. AVAILABILITY AND IMPLEMENTATION R source code for the method is available upon request.

PFAAT version 2.0: A tool for editing, annotating, and analyzing multiple sequence alignments

BackgroundBy virtue of their shared ancestry, homologous sequences are similar in their structure and function. Consequently, multiple sequence alignments are routinely used to identify trends that relate to function. This type of analysis is particularly productive when it is combined with structural and phylogenetic analysis.ResultsHere we describe the release of PFAAT version 2.0, a tool for editing, analyzing, and annotating multiple sequence alignments. Support for multiple annotations is a key component of this release as it provides a framework for most of the new functionalities. The sequence annotations are accessible from the alignment and tree, where they are typically used to label sequences or hyperlink them to related databases. Sequence annotations can be created manually or extracted automatically from UniProt entries. Once a multiple sequence alignment is populated with sequence annotations, sequences can be easily selected and sorted through a sophisticated search dialog. The selected sequences can be further analyzed using statistical methods that explicitly model relationships between the sequence annotations and residue properties. Residue annotations are accessible from the alignment viewer and are typically used to designate binding sites or properties for a particular residue.Residue annotations are also searchable, and allow one to quickly select alignment columns for further sequence analysis, e.g. computing percent identities. Other features include: novel algorithms to compute sequence conservation, mapping conservation scores to a 3D structure in Jmol, displaying secondary structure elements, and sorting sequences by residue composition.ConclusionPFAAT provides a framework whereby end-users can specify knowledge for a protein family in the form of annotation. The annotations can be combined with sophisticated analysis to test hypothesis that relate to sequence, structure and function.

Beyond data integration

Pharmaceutical R&D organizations have no shortage of experimental data or annotation information. However, the sheer volume and complexity of this information results in a paralyzing inability to make effective use of it for predicting drug efficacy and safety. Data integration efforts are legion, but even in the rare instances where they succeed, they are found to be insufficient to advance programs because interpretation of query results becomes a research project in itself. In this review, we propose a coherent, interoperable platform comprising knowledge engineering and hypothesis generation components for rapidly making determinations of confidence in mechanism and safety (among other goals) using experimental data and expert knowledge.

Construction of a sequence motif characteristic of aminergic G protein–coupled receptors

An approach to discover sequence patterns characteristic of ligand classes is described and applied to aminergic G protein–coupled receptors (GPCRs). Putative ligand‐binding residue positions were inferred from considering three lines of evidence: conservation in the subfamily absent or underrepresented in the superfamily, any available mutation data, and the physicochemical properties of the ligand. For aminergic GPCRs, the motif is composed of a conserved aspartic acid in the third transmembrane (TM) domain (rhodopsin position 117) and a conserved tryptophan in the seventh TM domain (rhodopsin position 293); the roles of each are readily justified by molecular modeling of ligand‐receptor interactions. This minimally defined motif is an appropriate computational tool for identifying additional, potentially novel aminergic GPCRs from a set of experimentally uncharacterized “orphan” GPCRs, complementing existing sequence matching, clustering, and machine‐learning techniques. Motif sensitivity stems from the stepwise addition of residues characteristic of an entire class of ligand (and not tailored for any particular biogenic amine). This sensitivity is balanced by careful consideration of residues (evidence drawn from mutation data, correlation of ligand properties to residue properties, and location with respect to the extracellular face), thereby maintaining specificity for the aminergic class. A number of orphan GPCRs assigned to the aminergic class by this motif were later discovered to be a novel subfamily of trace amine GPCRs, as well as the successful classification of the histamine H4 receptor.

Protein family annotation in a multiple alignment viewer

SUMMARY The Pfaat protein family alignment annotation tool is a Java-based multiple sequence alignment editor and viewer designed for protein family analysis. The application merges display features such as dendrograms, secondary and tertiary protein structure with SRS retrieval, subgroup comparison, and extensive user-annotation capabilities. AVAILABILITY The program and source code are freely available from the authors under the GNU General Public License at http://www.pfizerdtc.com

Accuracy of side-chain prediction upon near-native protein backbones generated by Ab initio folding methods.

The ab initio folding problem can be divided into two sequential tasks of approximately equal computational complexity: the generation of native‐like backbone folds and the positioning of side chains upon these backbones. The prediction of side‐chain conformation in this context is challenging, because at best only the near‐native global fold of the protein is known. To test the effect of displacements in the protein backbones on side‐chain prediction for folds generated ab initio, sets of near‐native backbones (≤ 4 Å Cα RMS error) for four small proteins were generated by two methods. The steric environment surrounding each residue was probed by placing the side chains in the native conformation on each of these decoys, followed by torsion‐space optimization to remove steric clashes on a rigid backbone. We observe that on average 40% of the χ1 angles were displaced by 40° or more, effectively setting the limits in accuracy for side‐chain modeling under these conditions. Three different algorithms were subsequently used for prediction of side‐chain conformation. The average prediction accuracy for the three methods was remarkably similar: 49% to 51% of the χ1 angles were predicted correctly overall (33% to 36% of the χ1+2 angles). Interestingly, when the inter‐side‐chain interactions were disregarded, the mean accuracy increased. A consensus approach is described, in which side‐chain conformations are defined based on the most frequently predicted χ angles for a given method upon each set of near‐native backbones. We find that consensus modeling, which de facto includes backbone flexibility, improves side‐chain prediction: χ1 accuracy improved to 51–54% (36–42% of χ1+2). Implications of a consensus method for ab initio protein structure prediction are discussed. Proteins 33:204–217, 1998.