De novo synthesis of oligosaccharides using a palladium-catalyzed glycosylation reaction

The natural all d- and/or unnatural all l-1,4- and 1,6-oligosaccharides were synthesized from furan alcohols using a palladium-catalyzed glycosylation reaction. The 1,4- and 1,6-alpha-manno-disaccharides were achieved in seven total steps starting from chiral furan alcohols. Similarly, 1,4- and 1,6-alpha-manno-trisaccharides were also synthesized in nine total steps. Key to the overall efficiency of this process was the use of highly diastereoselective palladium-catalyzed glycosylations, reductions, and dihydroxylations.     

Deterministic global optimization of molecular structures using interval analysis

The search for the global minimum of a molecular potential energy surface is a challenging problem. The molecular structure corresponding to the global minimum is of particular importance because it usually dictates both the physical and chemical properties of the molecule. The existence of an extremely large number of local minima, the number of which may increase exponentially with the size of the molecule, makes this global minimization problem extremely difficult. A new strategy is described here for solving such global minimization problems deterministically. The methodology is based on interval analysis, and provides a mathematical and computational guarantee that the molecular structure with the global minimum potential energy will be found. The technique is demonstrated using two sets of example problems. The first set involves a relatively simple potential model, and problems with up to 40 atoms. The second set involves a more realistic potential energy function, representative of those in current use, and problems with up to 11 atoms.     

De novo design and molecular assembly of a transmembrane diporphyrin-binding protein complex

The de novo design of membrane proteins remains difficult despite recent advances in understanding the factors that drive membrane protein folding and association. We have designed a membrane protein PRIME (PoRphyrins In MEmbrane) that positions two non-natural iron diphenylporphyrins (Fe(III)DPP's) sufficiently close to provide a multicentered pathway for transmembrane electron transfer. Computational methods previously used for the design of multiporphyrin water-soluble helical proteins were extended to this membrane target. Four helices were arranged in a D(2)-symmetrical bundle to bind two Fe(II/III) diphenylporphyrins in a bis-His geometry further stabilized by second-shell hydrogen bonds. UV-vis absorbance, CD spectroscopy, analytical ultracentrifugation, redox potentiometry, and EPR demonstrate that PRIME binds the cofactor with high affinity and specificity in the expected geometry.     

De novo sequencing of peptides using MALDI/TOF-TOF

The recently developed MALDI TOF-TOF instrument yields relatively complex but interpretable fragmentation spectra. When coupled with a straightforward sequence extension algorithm, it is possible to develop complete peptide sequences de novo from the spectra. This approach has been applied to a set of peptides derived from typtic digestion of electrophoretically separated sea urchin egg membrane proteins. When directed to proteins that have been described previously, the results were in essential agreement with those obtained by conventional data base searching approaches, with certain important exceptions. The present method detected errors in published sequences and was able to develop sequences from peptides differing in mass by one dalton (Da). These results show both the power of the present approach and the need for using de novo methods more frequently than may be otherwise appreciated.     

De novo synthesis of thiophenes on a polymeric support

The Hinsberg thiophene synthesis was expanded to support bound thioglycolic acid derived synthons, which reacted with arils to give thiophenes in high purity.     

De novo prediction of the structures of M. tuberculosis membrane proteins

The structures of four integral membrane proteins from the Mycobacterium tuberculosis (TB) gene, Rv2433c, Rv1861, Rv1616, and Rv3069, have been de novo predicted by combining a generalized Born implicit solvent/membrane model with replica exchange molecular dynamics simulations to sample the conformational space of each protein.     

De novo peptide sequencing using exhaustive enumeration of peptide composition

We introduce the use of a peptide composition lookup table indexed by residual mass and number of amino acids for de novo sequencing of polypeptides. Polypeptides of 1600 Daltons (Da) or more can be sequenced effectively through exhaustive compositional analysis of MS/MS spectra obtained by unimolecular decomposition (without CID) in a MALDI TOF/TOF despite a fragment mass accuracy of 50 mDa. Peaks are referenced against the lookup table to obtain a complete profile of amino acid combinations, and combinations are assembled into series of increasing length. Concatenating the differences between successive entries in compositional series yields peptide sequences that can be scored and ranked according to signal intensity. While the current work involves measurements acquired on MALDI TOF-TOF, such general treatment of the data anticipates extension to other types of mass analyzers.     

De novo design of a single-chain diphenylporphyrin metalloprotein

We describe the computational design of a single-chain four-helix bundle that noncovalently self-assembles with fully synthetic non-natural porphyrin cofactors. With this strategy, both the electronic structure of the cofactor as well as its protein environment may be varied to explore and modulate the functional and photophysical properties of the assembly. Solution characterization (NMR, UV-vis) of the protein showed that it bound with high specificity to the desired cofactors, suggesting that a uniquely structured protein and well-defined site had indeed been created. This provides a genetically expressed single-chain protein scaffold that will allow highly facile, flexible, and asymmetric variations to enable selective incorporation of different cofactors, surface-immobilization, and introduction of spectroscopic probes.     

Modulated structures on a square lattice

The lattice-gas model with competing interactions is studied using a cluster approximation for the transfer-matrix formalism. The model exhibits a very rich phase diagram which is obtained numerically and analyzed in detail.     

De novo generation of a bright blue fluorophore from 2-oxoglutarate in biological samples

We discovered the generation of a new bright blue fluorophore from a particular type of amine and 2-oxoglutarate (2-OG) under mild conditions without any chemical additives. Two β-aminoethylamine molecules and three 2-OG molecules form an unprecedented 2-pyridone structure with a fused γ-lactam ring (DTPP) via complex reactions including double decarboxylation and quintuple dehydration. The DTPP fluorophore shows a high quantum yield (80%) and photostability. The great potential of the present DTPP generation in the quantitative analysis of 2-OG in biosamples is demonstrated.

DTPP, a bright fluorophore with 2-pyridone and γ-lactam, is generated in a de novo manner from non-fluorogenic 2-oxoglutarate and specific amines. The DTPP-based fluorometry is applied to the analysis of 2-oxoglutarate in a biological sample.     

De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks

An evolutionary algorithm was developed for fragment-based de novo design of molecules (TOPAS, TOPology-Assigning System). This stochastic method aims at generating a novel molecular structure mimicking a template structure. A set of 25,000 fragment structures serves as the building block supply, which were obtained by a straightforward fragmentation procedure applied to 36,000 known drugs. Eleven reaction schemes were implemented for both fragmentation and building block assembly. This combination of drug-derived building blocks and a restricted set of reaction schemes proved to be a key for the automatic development of novel, synthetically tractable structures. In a cyclic optimization process, molecular architectures were generated from a parent structure by virtual synthesis, and the best structure of a generation was selected as the parent for the subsequent TOPAS cycle. Similarity measures were used to define `fitness', based on 2D-structural similarity or topological pharmacophore distance between the template molecule and the variants. The concept of varying library `diversity' during a design process was consequently implemented by using adaptive variant distributions. The efficiency of the design algorithm was demonstrated for the de novo construction of potential thrombin inhibitors mimicking peptide and non-peptide template structures.     

Multi-objective de novo molecular design of organic structure-directing agents for zeolites using nature-inspired ant colony optimization

Organic structure-directing agents (OSDAs) are often employed for synthesis of zeolites with desired frameworks. A priori prediction of such OSDAs has mainly relied on the interaction energies between OSDAs and zeolite frameworks, without cost considerations. For practical purposes, the cost of OSDAs becomes a critical issue. Therefore, the development of a computational de novo prediction methodology that can speed up the trial-and-error cycle in the search for less expensive OSDAs is desired. This study utilized a nature-inspired ant colony optimization method to predict physicochemically and/or economically preferable OSDAs, while also taking molecular similarity and heuristics of zeolite synthesis into consideration. The prediction results included experimentally known OSDAs, candidates having structures closely related to known OSDAs, and novel ones, suggesting the applicability of this approach.

Inspired by the exploratory methods of ant colonies, adaptive optimization was employed to explore the chemical space for organic molecules that guide zeolite crystallization, giving both physicochemically and economically promising molecules.     

De novo design of a stable N-terminal helical foldamer

A peptide NTH-18 was synthesized in which a N-terminal helix is stabilised by two crossed disulfide bonds to a C-terminal extension. The design was inspired by the structure of the neurotoxic peptide apamin, which has previously been used to stabilise helices in miniature enzymes. CD- and NMR-spectroscopy indicated that NTH-18 adopted a fold similar to that found in apamin. However, the arrangement of the elements of secondary structures was inverted relative to apamin; a N-terminal alpha-helix was connected by a reverse turn to a C-terminal extension of non-canonical secondary structure. NTH-18 displayed significant stability to heat and changes of pH. The high definition of the N-terminal end of the alpha-helix of NTH-18 should make this peptide a useful vehicle to stabilise alpha-helices in proteins with applications in protein engineering and molecular recognition.     

De novo design of a redox-active minimal rubredoxin mimic

Metal-binding sites in metalloproteins frequently occur at the interfaces of elements of secondary structure, which has enabled the retrostructural analysis of natural proteins and the de novo design of helical bundles that bind metal ion cofactors. However, the design of metalloproteins containing beta-structure is less well developed, despite the frequent occurrence of beta-conformations in natural metalloproteins. Here, we describe the design and construction of a beta-protein, RM1, that forms a stable, redox-active 4-Cys thiolate Fe(II/III) site analogous to the active site of rubredoxin. The protein folds into a beta-structure in the presence and absence of metal ions and binds Fe(II/III) to form a redox-active site that is stable to repeated cycles of oxidation and reduction, even in an aerobic environment.     

Minimal energy of unicyclic graphs of a given diameter

The energy of a graph is defined as the sum of the absolute values of all the eigenvalues of the graph. For a given positive integer d with , we characterize the graphs with minimal energy in the class of unicyclic graphs with n vertices and a given diameter d.      

De novo asymmetric synthesis of homoadenosine via a palladium-catalyzed N-glycosylation

[reaction: see text] A highly stereoselective synthesis of l-2-deoxy-beta-ribo-hexopyranosyl nucleosides from 6-chloropurine and Boc-protected pyranone has been developed. Our approach relies on the iterative application of a palladium-catalyzed N-glycosylation, diastereoselective reduction, and reductive 1,3-transposition. This strategy is amenable to prepare various natural and unnatural hexopyranosyl nucleosides analogues.     

De novo synthesis of deoxy sugar via a Wharton rearrangement

A highly divergent synthesis of α-fuco-, α-6-deoxy-allo-, α-6-deoxy-altro-pyranosides has been achieved. This route utilizes a Wharton rearrangement as part of a new post-glycosylation transformation strategy.     

De novo determination of protein backbone structure from residual dipolar couplings using Rosetta

As genome-sequencing projects rapidly increase the database of protein sequences, the gap between known sequences and known structures continues to grow exponentially, increasing the demand to accelerate structure determination methods. Residual dipolar couplings (RDCs) are an attractive source of experimental restraints for NMR structure determination, particularly rapid, high-throughput methods, because they yield both local and long-range orientational information and can be easily measured and assigned once the backbone resonances of a protein have been assigned. While very extensive RDC data sets have been used to determine the structure of ubiquitin, it is unclear to what extent such methods will generalize to larger proteins with less complete data sets. Here we incorporate experimental RDC restraints into Rosetta, an ab initio structure prediction method, and demonstrate that the combined algorithm provides a general method for de novo determination of a variety of protein folds from RDC data. Backbone structures for multiple proteins up to approximately 125 residues in length and spanning a range of topological complexities are rapidly and reproducibly generated using data sets that are insufficient in isolation to uniquely determine the protein fold de novo, although ambiguities and errors are observed for proteins with symmetry about an axis of the alignment tensor. The models generated are not high-resolution structures completely defined by experimental data but are sufficiently accurate to accelerate traditional high-resolution NMR structure determination and provide structure-based functional insights.     

The atom assignment problem in automated de novo drug design. 3. Algorithms for optimization of fragment placement onto 3D molecular graphs

Summary Atom assignment onto 3D molecular graphs is a combinatoric problem in discrete space. If atoms are to be placed efficiently on molecular graphs produced in drug binding sites, the assignment must be optimized. An algorithm, based on simulated annealing, is presented for efficient optimization of fragment placement. Extensive tests of the method have been performed on five ligands taken from the Protein Data Bank. The algorithm is presented with the ligand graph and the electrostatic potential as input. Self placement of molecular fragments was monitored as an objective test. A hydrogen-bond option was also included, to enable the user to highlight specific needs. The algorithm performed well in the optimization, with successful replications. In some cases, a modification was necessary to reduce the tendency to give multiple halogenated structures. This optimization procedure should prove useful for automated de novo drug design.