PRO_LIGAND: An approach to de novo molecular design. 3. A genetic algorithm for structure refinement

Summary Recently, the development of computer programs which permit the de novo design of molecular structures satisfying a set of steric and chemical constraints has become a burgeoning area of research and many operational systems have been reported in the literature. Experience with PRO_LIGAND—the de novo design methodology embodied in our in-house molecular design and simulation system PRO-METHEUS—has suggested that the addition of a genetic algorithm (GA) structure refinement procedure can add value to an already useful tool. Starting with the set of designed molecules as an initial population, the GA can combine features from both high- and low-scoring structures and, over a number of generations, produce individuals of better score than any of the starting structures. This paper describes how we have implemented such a procedure and demonstrates its efficacy in improving two sets of molecules generated by different de novo design projects.     

HostDesigner: a program for the de novo structure-based design of molecular receptors with binding sites that complement metal ion guests

This paper describes a novel approach to the discovery of host structures with binding sites that complement targeted metal ion guests. This approach uses a de novo structure-based design strategy that couples molecular building algorithms with scoring functions to prioritize candidate structures. The algorithms described herein have been implemented in a program called HostDesigner, the first structure-based design software specifically created for the discovery of metal ion receptors. HostDesigner generates and evaluates millions of candidate structures within minutes, rapidly identifying three-dimensional architectures that position binding sites to provide an optimal interaction with the metal ion.     

BUILDER v.2: Improving the chemistry of a de novo design strategy

Summary Significant improvements have been made to the de novo drug design program BUILDER. The BUILDER strategy is to find molecule templates that bind tightly to hot spots in the target receptor, and then generate bridges to join these templates. In this paper, the bridging algorithm has been further developed to improve the chemical sense and diversity of the bridges, as well as the robustness of the technique. The improved algorithm is then applied to rebuild known bridges in methotrexate and HIV protease. Finally, the entire BUILDER approach is tested by rebuilding methotrexate de novo.     

Metastable ion studies. IX—Thermochemistry and ion structures among fragmentating ions,an electron impact and field ionization investigation

Metastable peak shapes, dimensions and relative abundances have been measured for the fragmentations ions were generated from but 1-ene, cis-and trans- but-2-ene, 2-methylpropene, methylcyclopropane and cyclobutane. Forward and reverse activation energies for the above reactions have been estimated and daughter ion structures proposed. The pathway for the consecutive reaction which generates the metastable peak (m/e 56 → m/e 53) is proposed to be Observations on metastable peaks for fourteen assorted daughter ion fragmentations are also presented and the thermochemistry and daughter ion structures for some of the reactions are discussed. Metastable peaks for the fragmentation of ions generated by field ionization are also described.     

Automated Antibody De Novo Sequencing and Its Utility in Biopharmaceutical Discovery

Applications of antibody de novo sequencing in the biopharmaceutical industry range from the discovery of new antibody drug candidates to identifying reagents for research and determining the primary structure of innovator products for biosimilar development. When murine, phage display, or patient-derived monoclonal antibodies against a target of interest are available, but the cDNA or the original cell line is not, de novo protein sequencing is required to humanize and recombinantly express these antibodies, followed by in vitro and in vivo testing for functional validation. Availability of fully automated software tools for monoclonal antibody de novo sequencing enables efficient and routine analysis. Here, we present a novel method to automatically de novo sequence antibodies using mass spectrometry and the Supernovo software. The robustness of the algorithm is demonstrated through a series of stress tests.

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Collision induced dissociations of radical cations

The collision induced dissociation spectra of ions generated by ionization or fragmentation of various samples reveal at least five non-decomposing structures. In contrast, the kinetic energy release measurements for the loss of carbon monoxide from the metastable ions are in agreement with the occurrence of a common reactive species. Isomerization into an ‘α,β-unsaturated aldehyde-like’ structure prior to fragmentation is proposed to accommodate these collision induced dissociation and mass analysed ion kinetic energy data. Some resuts suggest also that carbon monoxide loss from the phenol molecular ion may not occur via the cyclohexadienone tautomer.     

Lock-and-key motif as a concept for designing affinity adsorbents for protein purification

The lock-and-key (LAK) motif, a common structural moiety found in subunit interfaces of glutathione S-transferases (GSTs), plays an important role in biomolecular recognition and quaternary structure integrity. Inspection of the key structural features of the LAK motif prompted the de novo design and combinatorial synthesis of a 13-membered solid-phase ligand library, employing as a lead ligand the Phe-Trz-X structure, mimicking the LAK motif. 1,3,5-Triazine (Trz) was used as the scaffold for assembly, substituted with different LAK-mimetic amino acids. De novo ligand design was effected using bioinformatics and molecular modeling and based on mimicking the interactions of the LAK motif. The library of affinity adsorbents was assessed for binding corn and human serum proteomes and purified proteins of different structure and ligand binding specificity. The results showed remarkable differences in the binding specificity of LAK-mimetic adsorbents for a wide range of proteins, as a consequence of minor changes in ligand structure. One LAK-mimetic adsorbent was integrated in a single-step purification protocol for human monoclonal anti-human immunodeficiency virus 2F5 antibody (mAb 2F5) from spiked corn extract, affording high recovery and purity. The results demonstrate that the principle of natural recognition found in the lock-and-key motif, in combination with de novo combinatorial design, may lead to synthetic affinity ligands, useful in downstream processing and proteomic research.     

Protein Folding with a Reduced Model and Inaccurate Short‐Range Restraints

Summary: A reduced high‐coordination lattice protein model and the Replica Exchange Monte Carlo sampling were employed in de novo folding simulations of a set of representative small proteins. Three distinct situations were analyzed. In the first series of simulations, the folding was controlled purely by the generic force field of the model. In the second, a bias was introduced towards the theoretically predicted secondary structure. Finally, we superimposed soft restraints towards the native‐like local conformation of the backbone. The short‐range restraints used in these simulations are based on approximate values of ϕ and ψ dihedral angles, which may simulate restraints derived from inaccurate experimental measurements. Incorporating such data into the reduced model required developing a procedure, which transforms the ϕ and ψ coordinates into coordinates of the protein alpha carbon trace. It has been shown that such limited data are sufficient for de novo determination of three‐dimensional structures of small and topologically not too complex proteins.

Protein folding based on secondary structure prediction and simulated torsion angles data.     

Multifunctional Poly(N‐vinylcarbazole)‐Based Block Copolymers and their Nanofabrication and Photosensitizing Properties

The synthesis of poly(N‐vinylcarbazole)‐based block copolymers functionalized with rhenium diimine complexes or pendant terpyridine ligands is reported. The copolymers are synthesized by reversible addition–fragmentation chain transfer (RAFT) polymerization, and they exhibit interesting morphological properties as a result of the phase separation between different blocks. The rhenium complex polymer block may function as a photosensitizer, while the terpyridine‐containing polymer block can be used as the template for nanofabrication by selective deposition of zinc complexes.

     

Second-generation de novo design: a view from a medicinal chemist perspective

For computational de novo design, a general retrospective validation work is a very challenging task. Here we propose a comprehensive workflow to de novo design driven by the needs of computational and medicinal chemists and, at the same time, we propose a general validation scheme for this technique. The study was conducted combining a suite of already published programs developed within the framework of the NovoBench project, which involved three different pharmaceutical companies and four groups of developers. Based on 188 PDB protein–ligand complexes with diverse functions, the study involved the ligand reconstruction by means of a fragment-based de-novo design approach. The structure-based de novo search engine FlexNovo showed in five out of eight total cases the ability to reconstruct native ligands and to rank them in four cases out of five within the first five candidates. The generated structures were ranked according to their synthetic accessibilities evaluated by the program SYLVIA. This investigation showed that the final candidate molecules have about the same synthetic complexity as the respective reference ligands. Furthermore, the plausibility of being true actives was assessed through literature searches. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.

Complex Macromolecular Architectures by Reversible Addition Fragmentation Chain Transfer Chemistry: Theory and Practice

Reversible addition–fragmentation chain transfer (RAFT) chemistry can be effectively employed to construct macromolecular architectures of varying topologies. The present article explores the principle design routes to star, block, and comb polymers in the context of theoretical design criteria for the so‐called Z‐ and R‐group approaches. The specific advantages and disadvantages of each approach are underpinned by selected examples generated in the CAMD laboratories. In particular, we demonstrate how the modeling of full molecular weight distributions can be employed to guide the synthetic effort. We further explore the theory and practice of generating amphiphilic block copolymer structures and their self‐assembly. In addition, the article foreshadows how modern synthetic techniques that combine RAFT chemistry with highly orthogonal click chemistry can be employed as a powerful tool that furthers the enhancement of macromolecular design possibilities to generate block (star) copolymers of monomers with extremely disparate reactivities. Finally, the ability of RAFT chemistry to modify the surface of well‐defined nano‐ and microspheres as devices in biomedical application is detailed.

     

A case study of de novo sequence analysis of N-sulfonated peptides by MALDI TOF/TOF mass spectrometry

The simplicity and sensitivity of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry have increased its application in recent years. The most common method of "peptide mass fingerprint" analysis often does not provide robust identification. Additional sequence information, obtained by post-source decay or collision induced dissociation, provides additional constraints for database searches. However, de novo sequencing by mass spectrometry is not yet common practice, most likely because of the difficulties associated with the interpretation of high and low energy CID spectra. Success with this type of sequencing requires full sequence coverage and demands better quality spectra than those typically used for data base searching. In this report we show that full-length de novo sequencing is possible using MALDI TOF/TOF analysis. The interpretation of MS/MS data is facilitated by N-terminal sulfonation after protection of lysine side chains (Keough et al., Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 7131-7136). Reliable de novo sequence analysis has been obtained using sub-picomol quantities of peptides and peptide sequences of up to 16 amino acid residues in length have been determined. The simple, predictable fragmentation pattern allows routine de novo interpretation, either manually or using software. Characterization of the complete primary structure of a peptide is often hindered because of differences in fragmentation efficiencies and in specific fragmentation patterns for different peptides. These differences are controlled by various structural parameters including the nature of the residues present. The influence of the presence of internal Pro, acidic and basic residues on the TOF/TOF fragmentation pattern will be discussed, both for underivatized and guanidinated/sulfonated peptides.     

Light-emitting conjugated polymers with microporous network architecture: interweaving scaffold promotes electronic conjugation, facilitates exciton migration, and improves luminescence

Herein we report a strategy for the design of highly luminescent conjugated polymers by restricting rotation of the polymer building blocks through a microporous network architecture. We demonstrate this concept using tetraphenylethene (TPE) as a building block to construct a light-emitting conjugated microporous polymer. The interlocked network successfully restricted the rotation of the phenyl units, which are the major cause of fluorescence deactivation in TPE, thus providing intrinsic luminescence activity for the polymers. We show positive "CMP effects" that the network promotes π-conjugation, facilitates exciton migration, and improves luminescence activity. Although the monomer and linear polymer analogue in solvents are nonemissive, the network polymers are highly luminescent in various solvents and the solid state. Because emission losses due to rotation are ubiquitous among small chromophores, this strategy can be generalized for the de novo design of light-emitting materials by integrating the chromophores into an interlocked network architecture.     

De novo synthesis of uronic acid building blocks for assembly of heparin oligosaccharides

An efficient de novo synthesis of uronic acid building blocks is described. The synthetic strategy relies on the stereoselective elongation of thioacetal protected dialdehydes 12 a and 17. The dialdehydes are prepared from D-xylose, a cheap and commercially available source. A highly stereoselective MgBr(2)OEt(2)-mediated Mukaiyama aldol addition to C4-aldehyde 12 a is performed to obtain D-glucuronic acid building block 16, whereas L-iduronic acid building block 22 is prepared by MgBr(2)OEt(2)-mediated cyanation of C5-aldehyde 17. Synthesis of a heparin disaccharide demonstrates the utility of the de novo strategy for the assembly of glycosaminoglycan oligosaccharides.     

Ring system-based chemical graph generation for de novo molecular design

Generating chemical graphs in silico by combining building blocks is important and fundamental in virtual combinatorial chemistry. A premise in this area is that generated structures should be irredundant as well as exhaustive. In this study, we develop structure generation algorithms regarding combining ring systems as well as atom fragments. The proposed algorithms consist of three parts. First, chemical structures are generated through a canonical construction path. During structure generation, ring systems can be treated as reduced graphs having fewer vertices than those in the original ones. Second, diversified structures are generated by a simple rule-based generation algorithm. Third, the number of structures to be generated can be estimated with adequate accuracy without actual exhaustive generation. The proposed algorithms were implemented in structure generator Molgilla. As a practical application, Molgilla generated chemical structures mimicking rosiglitazone in terms of a two dimensional pharmacophore pattern. The strength of the algorithms lies in simplicity and flexibility. Therefore, they may be applied to various computer programs regarding structure generation by combining building blocks.     

Far-from-equilibrium fluctuations triggering RNA de novo synthesis

The fluctuations for very low total template concentration (5–10⁴ molecules/cm³) are calculated theoretically for a self-replicating RNA system catalyzed by highly purifiedQ replicase, by means of a center manifold stochastic treatment. The results provide an explanation of the experimental observation that at 0.15 mM nucleoside triphosphate concentration, no RNA can be synthesizedde novo, although the templatedirected synthesis proceeds normally. The role of intrinsic template fluctuations, under far-from-equilibrium conditions; in triggeringde novo (template-free) replication is elucidated.     

Search for improved host architectures: application of de novo structure-based design and high-throughput screening methods to identify optimal building blocks for multidentate ethers

This paper presents a computational approach to the deliberate design of improved host architectures. The approach, which involves the use of computer-aided design software, is illustrated by application to cation hosts containing multiple aliphatic ether oxygen binding sites. De novo molecule building software, HostDesigner, is interfaced with molecular mechanics software, GMMX, providing a tool for generating and screening millions of potential bidentate building block structures. Enhanced cation binding affinity can be achieved when highly organized building blocks are used to construct macrocyclic hosts.