Controlling the morphology of cross beta-sheet assemblies by rational design

Low molecular weight peptidomimetics with simple amphiphilic sequences can help to elucidate the structures of cross beta-sheet assemblies, such as amyloid fibrils. The peptidomimetics described herein comprise a dibenzofuran template, two peptide strands made up of alternating hydrophilic and hydrophobic residues, and carboxyl termini, each of which can be varied to probe the structural requirements for beta-sheet self-assembly processes. The dibenzofuran template positions the strands approximately 10 A apart, allowing corresponding hydrophobic side chains in the strands to pack into a collapsed U-shaped structure. This conformation is stabilized by hydrophobic interactions, not intramolecular hydrogen bonds. Intermolecular stacking of the collapsed peptidomimetics, enabled by intermolecular hydrogen bonding and hydrophobic interactions, affords 25-27 A wide protofilaments having a cross beta-sheet structure. Association of protofilaments, mediated by the dibenzofuran substructures and driven by the hydrophobic effect, affords 50-60 A wide filaments. These widths can be controlled by changing the length of the peptide strands. Further assembly of the filaments into fibrils or ribbons can be controlled by modification of the template, C-terminus, and buffer ion composition.     

Beta-strand flipping and slipping triggered by turn replacement reveal the opportunistic nature of beta-strand pairing

We investigated how the register between adjacent beta-strands is specified using a series of mutants of the single-layer beta-sheet (SLB) in Borrelia OspA. The single-layer architecture of this system eliminates structural restraints imposed by a hydrophobic core, enabling us to address this question. A critical turn (turn 9/10) in the SLB was replaced with a segment with an intentional structural mismatch. Its crystal structure revealed a one-residue insertion into the central beta-strand (strand 9) of the SLB. This insertion triggered a surprisingly large-scale structural rearrangement: (i) the central strand (strand 9) was shifted by one residue, causing the strand to flip with respect to the adjacent beta-strands and thus completely disrupting the native side-chain contacts; (ii) the three-residue turn located on the opposite end of the beta-strand (turn 8/9) was pushed into its preceding beta-strand (strand 8); (iii) the register between strands 8 and 9 was shifted by three residues. Replacing the original sequence for turn 8/9 with a stronger turn motif restored the original strand register but still with a flipped beta-strand 9. The stability differences of these distinct structures were surprisingly small, consistent with an energy landscape where multiple low-energy states with different beta-sheet configurations exist. The observed conformations can be rationalized in terms of maximizing the number of backbone H-bonds. These results suggest that adjacent beta-strands "stick" through the use of factors that are not highly sequence specific and that beta-strands could slide back and forth relatively easily in the absence of external elements such as turns and tertiary packing.     

Potential of fragment recombination for rational design of proteins

It is hypothesized that protein domains evolved from smaller intrinsically stable subunits via combinatorial assembly. Illegitimate recombination of fragments that encode protein subunits could have quickly led to diversification of protein folds and their functionality. This evolutionary concept presents an attractive strategy to protein engineering, e.g., to create new scaffolds for enzyme design. We previously combined structurally similar parts from two ancient protein folds, the (βα)(8)-barrel and the flavodoxin-like fold. The resulting "hopeful monster" differed significantly from the intended (βα)(8)-barrel fold by an extra β-strand in the core. In this study, we ask what modifications are necessary to form the intended structure and what potential this approach has for the rational design of functional proteins. Guided by computational design, we optimized the interface between the fragments with five targeted mutations yielding a stable, monomeric protein whose predicted structure was verified experimentally. We further tested binding of a phosphorylated compound and detected that some affinity was already present due to an intact phosphate-binding site provided by one fragment. The affinity could be improved quickly to the level of natural proteins by introducing two additional mutations. The study illustrates the potential of recombining protein fragments with unique properties to design new and functional proteins, offering both a possible pathway of protein evolution and a protocol to rapidly engineer proteins for new applications.     

Heuristic lipophilicity potential for computer-aided rational drug design

In this contribution we suggest a heuristic molecular lipophilicitypotential (HMLP), which is a structure-based technique requiring noempirical indices of atomic lipophilicity. The input data used in thisapproach are molecular geometries and molecular surfaces. The HMLP is amodified electrostatic potential, combined with the averaged influences fromthe molecular environment. Quantum mechanics is used to calculate theelectron density function (r) and the electrostatic potential V(r), andfrom this information a lipophilicity potential L(r) is generated. The HMLPis a unified lipophilicity and hydrophilicity potential. The interactions ofdipole and multipole moments, hydrogen bonds, and charged atoms in amolecule are included in the hydrophilic interactions in this model. TheHMLP is used to study hydrogen bonds and water–octanol partitioncoefficients in several examples. The calculated results show that the HMLPgives qualitatively and quantitatively correct, as well as chemicallyreasonable, results in cases where comparisons are available. Thesecomparisons indicate that the HMLP has advantages over the empiricallipophilicity potential in many aspects. The HMLP is a three-dimensional andeasily visualizable representation of molecular lipophilicity, suggested asa potential tool in computer-aided three-dimensional drug design.     

A new tool for the rational design of methylbiotin hosts

To study the binding mode of biotin related compounds with artificial hosts, we have developed a new tool to be used as a guide to test their behaviour prior to their synthesis. In that way, we have considered a set of 23 complexes comprising biotin and urea derivatives with synthetic hosts to develop a Partial Least Squares Cross-Validated (PLS-CV) model. The data, for such a model, are the binding constants (K_b) of each complex and the interaction energies (−E_min) calculated by molecular mechanics with AMBER and OPLS force fields. The predictive power of the model has been verified.     

Toward a rational design of beta-peptide structures

Intrinsic conformational characteristics of beta-peptides built up from simple achiral and chiral beta-amino acid residues (i.e., HCO-beta-Ala-NH2, HCO-beta-Abu-NH2) were studied using quantum chemical calculations and 1H-NMR spectroscopy. A conformer-based systematic and uniform nomenclature was introduced to differentiate conformers. Geometry optimizations were performed on all homoconformers of both HCO-(beta-Ala)(k)-NH2 and HCO-(beta-Abu)(k)-NH2 (1 < or = k < or = 6) model systems at the RHF/3-21G and RHF/6-311++G(d, p) levels of theory. To test for accuracy and precision, additional computations were carried out at several levels of theory [e.g., RHF/6-31G(d), and B3LYP/6-311++G(d, p)]. To display the folding preference, the relative stability of selected conformers as function of the length of the polypeptide chain was determined. Ab initio population distribution of hexapeptides and the conformational ensemble of synthetic models composed of beta-Ala and beta-Abu studied using 1H-NMR in different solvents were compared at a range of temperatures. Helical preference induced by various steric effects of nonpolar side chains was tested using higher level ab initio methods for well-known model systems such as: HCO-(beta-HVal-beta-HAla-beta-HLeu)2-NH2, HCO-(ACHC)6-NH2, HCO-(trans-ACPC)6-NH2, and HCO-(cis-ACPC)6-NH2. The relative stabilities determined by theoretical methods agreed well with most experimental data, supporting the theory that the local conformational preference influenced by steric effects is a key determining factor of the global fold both in solution and in the gas phase.     

Trifluoromethyl-substituted hydantoins, versatile building blocks for rational drug design

Preparatively simple, one-pot syntheses of trifluoromethyl-substituted hydantoins starting from Boc-protected imines of hexafluoroacetone and trifluoropyruvate are described. They represent valuable building blocks for the construction of constrained peptides or as scaffolds for the synthesis of highly potent VLA-4 antagonists.     

Towards a rational spacer design for bivalent inhibition of estrogen receptor

Estrogen receptors are known drug targets that have been linked to several kinds of cancer. The structure of the estrogen receptor ligand binding domain is available and reveals a homodimeric layout. In order to improve the binding affinity of known estrogen receptor inhibitors, bivalent compounds have been developed that consist of two individual ligands linked by flexible tethers serving as spacers. So far, binding affinities of the bivalent compounds do not surpass their monovalent counterparts. In this article, we focus our attention on the molecular spacers that are used to connect the individual ligands to form bivalent compounds, and describe their thermodynamic contribution during the ligand binding process. We use computational methods to predict structural and entropic parameters of different spacer structures. We find that flexible spacers introduce a number of effects that may interfere with ligand binding and possibly can be connected to the low binding affinities that have been reported in binding assays. Based on these findings, we try to provide guidelines for the design of novel molecular spacers.     

Basic principles for rational design of high-performance nanostructured silicon-based thermoelectric materials

Recently, nanostructured silicon-based thermoelectric materials have drawn great attention owing to their excellent thermoelectric performance in the temperature range around 450 °C, which is eminently applicable for concentrated solar thermal technology. In this work, a unified nanothermodynamic model is developed to investigate the predominant factors that determine the lattice thermal conductivity of nanocrystalline, nanoporous, and nanostructured bulk Si. A systematic study shows that the thermoelectric performance of these materials can be substantially enhanced by the following three basic principles: 1) artificial manipulation and optimization of roughness with surface/interface patterning/engineering; 2) grain-size reduction with innovative fabrication techniques in a controllable fashion; and 3) optimization of material parameters, such as bulk solid-vapor transition entropy, bulk vibrational entropy, dimensionality, and porosity, to decrease the lattice thermal conductivity. These principles may be used to rationally design novel nanostructured Si-based thermoelectric materials for renewable energy applications.     

A general strategy for the rational design of size-selective mesoporous catalysts

A series of functionalized mesoporous silicas with cagelike pore topology has been synthesized and screened for size-selective catalytic transformations. The aluminum-catalyzed Meerwein-Ponndorf-Verley (MPV) reduction of differently sized aromatic aldehydes (benzaldehyde and 1-pyrenecarbox-aldehyde) has been investigated as a test reaction. The catalysts were synthesized in a two-step grafting sequence comprising pore-size engineering of mesoporous silicas (SBA-1, SBA-2, SBA-16) with long-chain alkyl dimethylaminosilanes and surface organoaluminum chemistry with triethylaluminum [{Al(CH(2)CH(3))3}2]. Size-selective reaction behavior was found for small pore SBA-1 materials, and the selectivity could be efficiently tuned by selecting a silylating reagent of appropriate size. The results are compared with the catalytic performance of a large-pore periodic mesoporous organosilica PMO[SBA-1] and the nonporous high-surface-area silicas Aerosil 300/380.     

Inverse quantum chemistry: Concepts and strategies for rational compound design

The rational design of molecules and materials is becoming more and more important. With the advent of powerful computer systems and sophisticated algorithms, quantum chemistry plays a decisive role in the design process. While traditional quantum chemical approaches predict the properties of a predefined molecular structure, the goal of inverse quantum chemistry is to find a structure featuring one or more desired properties. Herein, we review inverse quantum chemical approaches proposed so far and discuss their advantages as well as their weaknesses. © 2014 Wiley Periodicals, Inc.     

Toward rational design of complex nanostructured liquid crystals

An analogy of block copolymer micro‐segregation as a low‐molecular weight nanostructured liquid crystal (LC) was tested with recently found columnar and cubic phase‐forming LC molecules, to clarify the broader applicability of the analogy as a molecular design principle. We found that the copolymer analogy principle also works well for new micellar cubic phase‐forming molecules. For bicontinuous cubic phase‐forming 1,2‐bis(4′‐n‐alkoxybenzoyl)hydrazines (BABH‐n) compounds that cover a much broader core fraction range than that predicted by the copolymer analogy, we propose hierarchical preferential orientation as an additional mechanism for their cubic range broadening. For azo‐dichiral molecules that also do not fit with the above principle, we propose chiral segregation as an alternative origin for their cubic phase formation. DOI 10.1002/tcr.201000025     

Use of the tubulin bound paclitaxel conformation for structure-based rational drug design

A new computational docking protocol has been developed and used in combination with conformational information inferred from REDOR-NMR experiments on microtubule bound 2-(p-fluorobenzoyl)paclitaxel to delineate a unique tubulin binding structure of paclitaxel. A conformationally constrained macrocyclic taxoid bearing a linker between the C-14 and C-3'N positions has been designed and synthesized to enforce this "REDOR-taxol" conformation. The novel taxoid SB-T-2053 inhibits the growth of MCF-7 and LCC-6 human breast cancer cells (wild-type and drug resistant) on the same order of magnitude as paclitaxel. Moreover, SB-T-2053 induces in vitro tubulin polymerization at least as well as paclitaxel, which directly validates our drug design process. These results open a new avenue for drug design of next generation taxoids and other microtubule-stabilizing agents based on the refined structural information of drug-tubulin complexes, in accordance with typical enzyme-inhibitor medicinal chemistry precepts.     

ALS抑制剂合理分子设计的研究进展

以乙酰乳酸合成酶为靶标合理设计开发新型超高效除草剂是当前除草剂化学研究中的重要领域。结合本课题组的研究工作,从ALS抑制剂的结构特征、分子力学与量子化学研究、定量构效关系(QSAR)与三维定量构效关系(3D-QSAR)研究、非线性QSAR研究以及新型除草剂的分子设计等几个方面对该领域的研究现状进行了总结报道,并对该领域的发展前景及存在的问题进行了展望。     

The absence of favorable aromatic interactions between beta-sheet peptides

This paper asks whether interactions between phenylalanine (Phe) residues of the non-hydrogen-bonded cross-strand pairs of antiparallel beta-sheets are important and finds that they are not. Peptides 1a-d [o-BuO-C6H4CO-AA1-Orn(i-PrCO-Hao)-Phe-Ile-AA5-NHMe: 1a AA1, AA5 = Phe; 1b AA1, AA5 = Cha (cyclohexylalanine); 1c AA1 = Phe, AA5 = Cha; 1d AA1 = Cha, AA5 = Phe] provide a sensitive system for probing interactions between phenylalanine residues. These peptides form beta-sheet homodimers in organic solvents. When the homodimers of different peptides are mixed, they equilibrate to form heterodimers, as well as homodimers. The position of the equilibrium reflects the propensity of the first (AA1) and fifth (AA5) amino acids to interact within the non-hydrogen-bonded cross-strand pairs of beta-sheets. Mixing peptides 1a-d in all six possible binary combinations provides a measure of the relative propensities of Phe and Cha to pair. Analysis by 1H NMR spectroscopy of the equilibrium constants in CDCl3 solution reveals no significant preference for the formation of Phe-Phe pairs. The equilibria in all six experiments are essentially statistical (K approximately 4), and no (<0.1 kcal/mol) preference is seen for any pairing combination. A survey of Phe-Phe pairs in the Interchain beta-Sheet Database (http://www.igb.uci.edu/servers/icbs/) corroborates that little significant contact occurs between the aromatic rings in the non-hydrogen-bonded cross-strand pairs of antiparallel beta-sheets at the interface between polypeptide chains. Even though contacts between aromatic rings are favorable when they are of suitable geometry, the energetic price of achieving suitable geometries appears to offset the energetic benefits of such contacts in the current model system, as well as in proteins.     

GREEN: A program package for docking studies in rational drug design

Summary A program package, GREEN, has been developed that enables docking studies between ligand molecules and a protein molecule. Based on the structure of the protein molecule, the physical and chemical environment of the ligand-binding site is expressed as three-dimensional grid-point data. The grid-point data are used for the real-time evaluation of the protein-ligand interaction energy, as well as for the graphical representation of the binding-site environment. The interactive docking operation is facilitated by various built-in functions, such as energy minimization, energy contribution analysis and logging of the manipulation trajectory. Interactive modeling functions are incorporated for designing new ligand molecules while considering the binding-site environment and the protein-ligand interaction. As an example of the application of GREEN, a docking study is presented on the complex between trypsin and a synthetic trypsin inhibitor. The program package will be useful for rational drug design, based on the 3D structure of the target protein.