Jiri Vondrasek

MedusaScore: An accurate force field-based scoring function for virtual drug screening

Virtual screening is becoming an important tool for drug discovery. However, the application of virtual screening has been limited by the lack of accurate scoring functions. Here, we present a novel scoring function, MedusaScore, for evaluating protein-ligand binding. MedusaScore is based on models of physical interactions that include van der Waals, solvation, and hydrogen bonding energies. To ensure the best transferability of the scoring function, we do not use any protein-ligand experimental data for parameter training. We then test the MedusaScore for docking decoy recognition and binding affinity prediction and find superior performance compared to other widely used scoring functions. Statistical analysis indicates that one source of inaccuracy of MedusaScore may arise from the unaccounted entropic loss upon ligand binding, which suggests avenues of approach for further MedusaScore improvement.

HIVdb: A Database of the Structures of Human Immunodeficiency Virus Protease

Human immunodeficiency virus protease (HIV PR) was only discovered as encoded in the HIV genome in 1985, but soon thereafter, this virus-specific enzyme was identified as a crucial target for designing drugs against acquired human immunodeficiency syndrome (AIDS). With six such drugs approved to date since 1995 by the United States Food and Drug Administration and several others in current clinical trials, the initial promise of rational drug design that originally seemed to be overly optimistic has been fulfilled beyond expectations. Introduction of PR inhibitors has changed the clinical outcome of AIDS and transformed an invariably fatal disease into a manageable one, although serious side effects and the development of resistance are still major unsolved problems. Crystal structures of HIV PR were first reported in 1989 and their availability had a major role in the process of drug development (although it is clear that the structures provided only a small fragment of information necessary for drug design). All pharmaceutical companies that succeeded in creating PR inhibitor drugs and many that either discontinued the efforts or are still conducting such research have been involved in solving numerous crystal structures of HIV PR. Most of these structures were of complexes of the enzyme with inhibitors that were either potential or actual drugs, or intermediate compounds useful in drug-design efforts. In addition, many academic laboratories joined the field and solved crystal and nuclear magnetic resonance structures of the complexes of HIV-1, HIV-2, and simian immunodeficiency virus (SIV) PRs with many diverse inhibitors. Because many variants of these proteins are known, attributable either to natural variation in the viral genomes or to their rapid mutation as a result of drug resistance, numerous mutant structures were also solved in pharmaceutical and academic laboratories. Although the total number of structures of these enzymes is not known, it can be estimated at many hundreds, making HIV PR the most widely studied enzyme in the history of protein crystallography. During the last 13 years, many structures of HIV PR were published and as many as approximately 150 have been deposited at the Protein Data Bank (PDB). However, it became clear early on that many other structures, especially those solved as part of drug-development efforts and neither fully refined nor published, might ultimately be lost. This prompted the National Institute of General Medical Sciences (NIGMS) to award in 1996 an interagency agreement to the National Cancer Institute (NCI), where some of the initial structural efforts on HIV PR have taken place, to create a repository that would contain as many structures as possible, and not necessarily only the published ones. This decision led to creation of the Internetbased HIV PR Database (HIVdb). After 6 years spent on creating and curating this database, the NCI effort is terminating on September 30, 2002. After that date, the National Institute of Standards and Technology (NIST), in collaboration with PDB, will take over and continue the project. This change of guard seems to be an opportune moment to remind the community about the existence of the database and the associated tools that have been created to enable its utilization. HIVdb is an Internet-based archive of experimentally determined three-dimensional structures of HIV-1, HIV-2, and SIV PRs and their complexes with inhibitors or products of substrate cleavage. HIVdb was one of the first databases of macromolecular structures created outside of the PDB. HIVdb includes both primary structural data and the derived information for this family of three very closely related enzymes. For that reason, it serves as an example of a special subset of a general structural database that can exist on its own, as well as coexist with a larger structural database and its tools. Information regarding one particular enzyme can show in detail how the structure adapts to binding of different ligands through changes in protein–ligand interactions, and conformationally adjusts to binding under different conditions. For proteins that serve as drug-design targets, it is important to study these interactions fully and in as many complexes as possible. Careful analysis of the wild-type as well as drug-resistant mutants of HIV PR may also help in creating new drugs that would overcome the problem of resistance. The structures contained in HIVdb have either been previously deposited in the PDB, or have been obtained directly from depositors for their inclusion in HIVdb only. In the latter case, they may have been less completely refined, or even not refined at all beyond the placement of the ligand; or they may have resulted from experiments that were never fully completed and published, but nevertheless were comparable in quality to the structures deposited in PDB. Many structures unique to HIVdb came

Metadynamics As a Tool for Mapping the Conformational and Free-Energy Space of Peptides — The Alanine Dipeptide Case Study

There is a need for a fast, accurate, and reliable method of sampling the conformational space of peptides and proteins in order to obtain a balanced free-energy profile which can lead to our understanding of protein structure. We have utilized metadynamics for the conformational study of the solvated alanine dipeptide molecule, and our results show that the method has proven to be competent as a fast, robust, and reliable method for the conformation free-energy calculations of peptides in an explicit solvent, surpassing traditional methods such as umbrella sampling. We have also addressed the issue of the influence of different water models on the resulting free-energy profile in order to consistently decompose the setting of our simulation. All of the explicit water models for the simulation of biomolecules TIP3P, TIP4P, TIP4P/Ew, TIP5P, and SPCE have exhibited similar effects on the conformational preferences of alanine dipeptide with no significant differences. On the other hand, by comparing the potential energy surface in the gas phase and the free-energy surface in a water environment, we have shown that the interaction with water molecules is one of the most important structure-driving elements, with a great influence on the free-energy surface (FES) of the solvated peptide and the conformational preferences of the peptide backbone. All of the tested force fields (ff03, ff99SB, opls-aa, and charmm27) appreciably differ in the population of the individual conformers and the barriers between them. Significant divergence was found on both the potential energy surface (PES) as well as free-energy surface (FES) calculated by charmm27. We have therefore concluded that the differences originate dominantly from the parametrization of the peptide backbone in the given force field rather than from a noncovalent interaction with water molecules.

Application of InChI to curate, index, and query 3-D structures†‡

The HIV structural database (HIVSDB) is a comprehensive collection of the structures of HIV protease, both of unliganded enzyme and of its inhibitor complexes. It contains abstracts and crystallographic data such as inhibitor and protein coordinates for 248 data sets, of which only 141 are from the Protein Data Bank (PDB). Efficient annotation, indexing, and querying of the inhibitor data is crucial for their effective use for technological and industrial applications. The application of IUPAC International Chemical Identifier (InChI) to index, curate, and query inhibitor structures HIVSDB is described. Proteins 2005. Published 2005 Wiley‐Liss, Inc.

Intrinsically Disordered Enamel Matrix Protein Ameloblastin Forms Ribbon-like Supramolecular Structures via an N-terminal Segment Encoded by Exon 5

Background: Ameloblastin plays a key role in the complex biomineralization process that forms tooth enamel, the hardest tissue of the body. Results: Ameloblastin self-associates into ribbon-like supramolecular structures via a short segment encoded by exon 5. Conclusion: Ameloblastin self-association may be essential for correct structural organization and mineralization of the enamel in vivo. Significance: The results provide molecular insight into biology of tooth enamel formation. Tooth enamel, the hardest tissue in the body, is formed by the evolutionarily highly conserved biomineralization process that is controlled by extracellular matrix proteins. The intrinsically disordered matrix protein ameloblastin (AMBN) is the most abundant nonamelogenin protein of the developing enamel and a key element for correct enamel formation. AMBN was suggested to be a cell adhesion molecule that regulates proliferation and differentiation of ameloblasts. Nevertheless, detailed structural and functional studies on AMBN have been substantially limited by the paucity of the purified nondegraded protein. With this study, we have developed a procedure for production of a highly purified form of recombinant human AMBN in quantities that allowed its structural characterization. Using size exclusion chromatography, analytical ultracentrifugation, transmission electron, and atomic force microscopy techniques, we show that AMBN self-associates into ribbon-like supramolecular structures with average widths and thicknesses of 18 and 0.34 nm, respectively. The AMBN ribbons exhibited lengths ranging from tens to hundreds of nm. Deletion analysis and NMR spectroscopy revealed that an N-terminal segment encoded by exon 5 comprises two short independently structured regions and plays a key role in self-assembly of AMBN.

Chemical Compound Navigator: A Web-Based Chem-BLAST, Chemical Taxonomy-Based Search Engine for Browsing Compounds

A novel technique to annotate, query, and analyze chemical compounds has been developed and is illustrated by using the inhibitor data on HIV protease‐inhibitor complexes. In this method, all chemical compounds are annotated in terms of standard chemical structural fragments. These standard fragments are defined by using criteria, such as chemical classification; structural, chemical, or functional groups; and commercial, scientific or common names or synonyms. These fragments are then organized into a data tree based on their chemical substructures. Search engines have been developed to use this data tree to enable query on inhibitors of HIV protease (http://xpdb.nist.gov/hivsdb/hivsdb.html). These search engines use a new novel technique, Chemical Block Layered Alignment of Substructure Technique (Chem‐BLAST) to search on the fragments of an inhibitor to look for its chemical structural neighbors. This novel technique to annotate and query compounds lays the foundation for the use of the Semantic Web concept on chemical compounds to allow end users to group, sort, and search structural neighbors accurately and efficiently. During annotation, it enables the attachment of “meaning” (i.e., semantics) to data in a manner that far exceeds the current practice of associating “metadata” with data by creating a knowledge base (or ontology) associated with compounds. Intended users of the technique are the research community and pharmaceutical industry, for which it will provide a new tool to better identify novel chemical structural neighbors to aid drug discovery. Proteins 2006.

PIP2 and PIP3 interact with N-terminus region of TRPM4 channel

The transient receptor potential melastatin 4 (TRPM4) is a calcium-activated non-selective ion channel broadly expressed in a variety of tissues. Receptor has been identified as a crucial modulator of numerous calcium dependent mechanisms in the cell such as immune response, cardiac conduction, neurotransmission and insulin secretion. It is known that phosphoinositide lipids (PIPs) play a unique role in the regulation of TRP channel function. However the molecular mechanism of this process is still unknown. We characterized the binding site of PIP2 and its structural analogue PIP3 in the E733-W772 proximal region of the TRPM4 N-terminus via biophysical and molecular modeling methods. The specific positions R755 and R767 in this domain were identified as being important for interactions with PIP2/PIP3 ligands. Their mutations caused a partial loss of PIP2/PIP3 binding specificity. The interaction of PIP3 with TRPM4 channels has never been described before. These findings provide new insight into the ligand binding domains of the TRPM4 channel.

Characterization of the part of N-terminal PIP2 binding site of the TRPM1 channel.

Transient receptor potential melastatin-1 (TRPM1) is a calcium channel that is essential for the depolarization of photo-responsive retinal bipolar cells, but most of the physiological functions and cellular roles of this channel are still poorly understood. Most transient receptor potential (TRP) channels are typically regulated by intracellular proteins and other signaling molecules. Phosphatidylinositol-4,5 bisphosphate (PIP2), a minor phospholipid component of cell membranes, has previously been shown to directly bind TRP channels and to play a unique role in modulating receptor function. To characterize the binding of PIP2 as a potential regulator of TRPM1, we utilized biophysical methods and molecular modeling to study the interactions of PIP2 with an N-terminal fragment of TRPM1 (residues A451-N566). The basic N-terminal residue K464 of TRPM1 suggests that it is part of putative pleckstrin homology (PH) domain and is involved in the interactions with PIP2. This is the first report detailing the binding of PIP2 at the N-terminus of the TRPM1 receptor.

Insights into Unfolded Proteins from the Intrinsic ϕ/ψ Propensities of the AAXAA Host-Guest Series

Various host-guest peptide series are used by experimentalists as reference conformational states. One such use is as a baseline for random-coil NMR chemical shifts. Comparison to this random-coil baseline, through secondary chemical shifts, is used to infer protein secondary structure. The use of these random-coil data sets rests on the perception that the reference chemical shifts arise from states where there is little or no conformational bias. However, there is growing evidence that the conformational composition of natively and nonnatively unfolded proteins fail to approach anything that can be construed as random coil. Here, we use molecular dynamics simulations of an alanine-based host-guest peptide series (AAXAA) as a model of unfolded and denatured states to examine the intrinsic propensities of the amino acids. We produced ensembles that are in good agreement with the experimental NMR chemical shifts and confirm that the sampling of the 20 natural amino acids in this peptide series is be far from random. Preferences toward certain regions of conformational space were both present and dependent upon the environment when compared under conditions typically used to denature proteins, i.e., thermal and chemical denaturation. Moreover, the simulations allowed us to examine the conformational makeup of the underlying ensembles giving rise to the ensemble-averaged chemical shifts. We present these data as an intrinsic backbone propensity library that forms part of our Structural Library of Intrinsic Residue Propensities to inform model building, to aid in interpretation of experiment, and for structure prediction of natively and nonnatively unfolded states.

Amino Acid Interaction (INTAA) web server

Abstract Large biomolecules—proteins and nucleic acids—are composed of building blocks which define their identity, properties and binding capabilities. In order to shed light on the energetic side of interactions of amino acids between themselves and with deoxyribonucleotides, we present the Amino Acid Interaction web server (http://bioinfo.uochb.cas.cz/INTAA/). INTAA offers the calculation of the residue Interaction Energy Matrix for any protein structure (deposited in Protein Data Bank or submitted by the user) and a comprehensive analysis of the interfaces in protein–DNA complexes. The Interaction Energy Matrix web application aims to identify key residues within protein structures which contribute significantly to the stability of the protein. The application provides an interactive user interface enhanced by 3D structure viewer for efficient visualization of pairwise and net interaction energies of individual amino acids, side chains and backbones. The protein–DNA interaction analysis part of the web server allows the user to view the relative abundance of various configurations of amino acid–deoxyribonucleotide pairs found at the protein–DNA interface and the interaction energies corresponding to these configurations calculated using a molecular mechanical force field. The effects of the sugar-phosphate moiety and of the dielectric properties of the solvent on the interaction energies can be studied for the various configurations.