Directed evolution of ATP binding proteins from a zinc finger domain by using mRNA display

Antibodies have traditionally been used for isolating affinity reagents to new molecular targets, but alternative protein scaffolds are increasingly being used for the directed evolution of proteins with novel molecular recognition properties. We have designed a combinatorial library based on the DNA binding domain of the human retinoid-X-receptor (hRXRalpha). We chose this domain because of its small size, stable fold, and two closely juxtaposed recognition loops. We replaced the two loops with segments of random amino acids, and used mRNA display to isolate variants that specifically recognize adenosine triphosphate (ATP), demonstrating a significant alteration of the function of this protein domain from DNA binding to ATP recognition. Many novel independent sequences were recovered with moderate affinity and high specificity for ATP, validating this scaffold for the generation of functional molecules.     

Solid-phase synthesis of tetrahydro-1,4-benzodiazepine-2-one derivatives as a beta-turn peptidomimetic library

The beta-turn has been implicated as an important conformation for biological recognition of peptides or proteins. We adapted the concept of general Calpha atom positioning from the cluster analysis and recombination of each ideal beta-turn conformation pattern by Garland and Dean (J. Comput.-Aided Mol. Des. 1999, 13, 469) as one strategy of designing non-peptide beta-turn scaffolds. Herein, the Calpha positions of tetrahydro-1,4-benzodiazepin-2-one scaffold were analyzed after the calculation of the low-energy conformer using a semiempirical protocol. Three points of corresponding Calpha carbons for diverse substitutions in the scaffold were designated, and an efficient solid-phase synthesis of the peptidomimetic library was developed. The scaffold itself was synthesized in solution phase starting from 5-hydroxy-2-nitrobenzaldehyde and loaded to the 4-formyl-3,5-dimethoxyphenoxy (PL-FDMP) resin with high efficiency of reductive amination. Various building blocks for the derivatization of the 7-hydroxyl and N-1 amide nitrogen could be introduced via selective alkylation. Cleavage, parallel column chromatography, and NMR analysis of 62 final compounds confirmed the feasibility of this peptidomimetic library synthesis.     

Synthesis of a constrained tricyclic scaffold based on trans-4-hydroxy-l-proline

Drug discovery research has taken advantage of peptidomimetic chemistry in order to achieve new leads possessing structural and functional characteristics of bioactive peptides together with enhanced metabolic resistance towards proteases. Herein is reported the synthesis of a tricyclic peptidomimetic scaffold derived from the combination of trans-4-hydroxy-l-proline and tartaric acid derivatives by means of amidation and acid trans-acetalisation reactions. Further manipulations of the hydroxylic function on the pyrrolidine ring gave access to a new set of amino acid scaffolds possessing high rigidity and a fixed arrangement of the functional groups.     

Closing the side-chain gap in protein loop modeling

The success of structure-based drug design relies on accurate protein modeling where one of the key issues is the modeling and refinement of loops. This study takes a critical look at modeled loops, determining the effect of re-sampling side-chains after the loop conformation has been generated. The results are evaluated in terms of backbone and side-chain conformations with respect to the native loop. While models can contain loops with high quality backbone conformations, the side-chain orientations could be poor, and therefore unsuitable for ligand docking and structure-based design. In this study, we report on the ability to model loop side-chains accurately using a variety of commercially available algorithms that include rotamer libraries, systematic torsion scans and knowledge-based methods. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Scaffold diversity of exemplified medicinal chemistry space

The scaffold diversity of 7 representative commercial and proprietary compound libraries is explored for the first time using both Murcko frameworks and Scaffold Trees. We show that Level 1 of the Scaffold Tree is useful for the characterization of scaffold diversity in compound libraries and offers advantages over the use of Murcko frameworks. This analysis also demonstrates that the majority of compounds in the libraries we analyzed contain only a small number of well represented scaffolds and that a high percentage of singleton scaffolds represent the remaining compounds. We use Tree Maps to clearly visualize the scaffold space of representative compound libraries, for example, to display highly populated scaffolds and clusters of structurally similar scaffolds. This study further highlights the need for diversification of compound libraries used in hit discovery by focusing library enrichment on the synthesis of compounds with novel or underrepresented scaffolds.     

Synthesis and structure of spirocyclic tetraethers derived from [1,1'-binaphthalene]-2,2'-diol and pentaerythritol

Molecular scaffolds that have well-defined geometries, are easy to synthesize and functionalize, and can hold attached sites of molecular recognition in suitable orientations are useful tools in various areas of science and technology. The utility of the tetraphenyl ether of pentaerythritol (4) as a scaffold in crystal engineering led us to study rigidified analogue SBINOX (5), the spirocyclic tetraether derived from pentaerythritol and [1,1'-binaphthalene]-2,2'-diol (BINOL). We have found that SBINOX (5) and derivatives can be prepared conveniently in acceptable yields and in stereoisomerically pure (S,S), (R,S), and (R,R) forms. X-ray crystallographic studies have revealed that the benzannulated 9-membered dioxonane rings in these structures adopt characteristic conformations of C1 symmetry. Intraannular C-H...O interactions help maintain the conformations of the individual rings, and the geometry of the spirocyclic SBINOX core is also controlled in part by distinctive short interannular C-H...O and C-H...pi interactions. Despite the inherent flexibility of the dioxonane rings, derivatives of SBINOX (5) can be expected to orient peripheral substituents in preferred ways, making SBINOX a potentially useful scaffold for applications in drug discovery, crystal engineering, and other fields.     

VISUALIZATION OF THE CHROMOSOME SCAFFOLD IN A PRIMITIVE EUKARYOTE DINOFLAGELLATE Crypthecoainium cohnii

The chromosome scaffolds in higher eukaryotic nuclei have been described elsewhere. Butit is unknown when they evolved. The dinoflagellates are the primitive organisms that maybe the intermediate between prokaryotes and eukaryotes. Combining chromosome scaffold prep-aration methods with embedment-free section microscopy,we demonstrate that the dino-flagellate Crypthecodinium cohnii chromosome retains a protein scaffold after the depletionof DNA and soluble proteins. This scaffold preserves the morphology characteristic of thechromosome. Two-dimensional electrophoreses show that the chromosome scaffolds are mainlycomposed of acidic proteins. Our results suggest that a framework similar to the chromosomescaffold in the mammalian cell appeared in the primitive eukaryote. We propose that thechromosome scaffold possibly originated from the early stages of eukaryote evolution.     

Anchor Residues Guide Form and Function in Grafted Peptides

Loops at protein–protein interfaces are a rich source of peptide leads that have high specificity and low toxicity. Although such peptides typically need to be constrained to overcome thermodynamic and metabolic limitations, design guidelines to obtain a successfully constrained peptides, and thus facilitate the transition from loop to drug, are relatively poorly formulated. In this work, we surveyed the structures of interface loops and found the position of the terminal residues to be a key determinant of conformation. We used this knowledge to improve the process of molecular grafting, a valuable approach for constraining and stabilising peptides by fusing them to a suitable scaffold. We show that an informed choice of where a loop is “anchored” to a scaffold improves its form and function. This knowledge can help guide the choice of loop and its matching scaffold, and thus increase the success rate for designing stable and potent peptide drug leads.     

Second-generation DNA-encoded multiple display on a constant macrocyclic scaffold enabled by an orthogonal protecting group strategy

DNA-encoded chemical library(DEL) represents an emerging drug discovery technology to construct compound libraries with abundant chemical combinations. While drug-like small molecule DELs facilitate the discovery of binders against targets with defined pockets, macrocyclic DELs harboring extended scaffolds enable targeting of the protein–protein interaction(PPI) interface. We previously demonstrated the design of the first-generation DNA-encoded multiple display based on a constant macrocyclic s...     

3D Plotted PCL Scaffolds for Stem Cell Based Bone Tissue Engineering

The ability to control the architecture and strength of a bone tissue engineering scaffold is critical to achieve a harmony between the scaffold and the host tissue. Rapid prototyping (RP) technique is applied to tissue engineering to satisfy this need and to create a scaffold directly from the scanned and digitized image of the defect site. Design and construction of complex structures with different shapes and sizes, at micro and macro scale, with fully interconnected pore structure and appropriate mechanical properties are possible by using RP techniques. In this study, RP was used for the production of poly(ε-caprolactone) (PCL) scaffolds. Scaffolds with four different architectures were produced by using different configurations of the fibers (basic, basic-offset, crossed and crossed-offset) within the architecture of the scaffold. The structure of the prepared scaffolds were examined by scanning electron microscopy (SEM), porosity and its distribution were analyzed by micro-computed tomography (µ-CT), stiffness and modulus values were determined by dynamic mechanical analysis (DMA). It was observed that the scaffolds had very ordered structures with mean porosities about 60%, and having storage modulus values about 1 × 10⁷ Pa. These structures were then seeded with rat bone marrow origin mesenchymal stem cells (MSCs) in order to investigate the effect of scaffold structure on the cell behavior; the proliferation and differentiation of the cells on the scaffolds were studied. It was observed that cell proliferation was higher on offset scaffolds (262000 vs 235000 for basic, 287000 vs 222000 for crossed structure) and stainings for actin filaments of the cells reveal successful attachment and spreading at the surfaces of the fibers. Alkaline phosphatase (ALP) activity results were higher for the samples with lower cell proliferation, as expected. Highest MSC differentiation was observed for crossed scaffolds indicating the influence of scaffold structure on cellular activities.     

DNA-guided display of proteins and protein ligands for the interrogation of biology

The self-assembly of nanosized DNA templates--based on formation of duplex, triplex, quadruplex or even pentaplex structures--provides unique opportunities for the controlled presentation of appended functional units. Recently, researchers have recognized the potential of such DNA scaffolds to address questions in the life sciences. In this critical review the focus is on the exploration of proteins. It is shown how different scaffolds can be used to control localization, structure and bioactivity of proteins and protein ligands. Further examples demonstrate that DNA-based recognition can even be used to trigger the formation of protein targeted molecules. Potential and existing applications in protein detection, drug discovery, structural characterization of protein targets as well as in the design of nucleic acid responsive pharmacophores are discussed (107 references).     

Target family-directed exploration of scaffolds with different SAR profiles

The scaffold concept is widely applied in chemoinformatics and medicinal chemistry to organize bioactive compounds according to common core structures or associate compound classes with specific biological activities. A variety of scaffold analyses have been carried out to derive statistics for scaffold distributions, generate structural organization schemes, or identify scaffolds that preferentially occur in given compound activity classes. Herein we further extend scaffold analysis by identifying scaffolds that display defined SAR profiles consisting of multiple properties. A structural relationship-based scaffold network has been designed as the basic data structure underlying our analysis. From network representations of scaffolds extracted from compounds active against 32 different target families, scaffolds with different SAR profiles have been extracted on the basis of decision trees that capture structural and functional characteristics of scaffolds in different ways. More than 600 scaffolds and 100 scaffold clusters were assigned to 10 SAR profiles. These scaffold sets represent different activity and target selectivity profiles and are provided for further SAR investigations including, for example, the exploration of alternative analog series for a given target of target family or the design of novel compounds on the basis of scaffold(s) with desired SAR profiles.     

Solid-phase synthesis of aspartic peptidase inhibitors: 3-alkoxy-4-aryl piperidines

[reaction: see text]. The 3-alkoxy-4-aryl piperidines are non-peptide peptidomimetic inhibitors of several aspartic peptidases. The solid-phase functionalization of 3,4-disubstituted piperidine scaffolds using a traceless linker strategy is described. Synthesis of diverse analogues based on this scaffold provides the potential to generate selective inhibitors of this important class of peptidase.     

An alpha-helical peptidomimetic inhibitor of the HIV-1 Rev-RRE interaction

The interaction between the HIV-1 Rev protein and the Rev-Responsive Element (RRE) RNA is an attractive target for anti-viral therapy. We have designed alpha-helical peptidomimetics of Rev-like peptides using side chain-side chain macrolactam formation between positions i and i+4. One peptidomimetic having an appropriate location, orientation, and length of the macrolactam exhibited both significant helical character and specific RRE binding. This molecule displays 2-fold greater RNA specificity than the wild-type Rev peptide and more than 20-fold greater specificity than an uncyclized control peptide. Thus, specific, high affinity recognition of the RRE is feasible utilizing a small, relatively rigid peptidomimetic scaffold.     

Tofu as excellent scaffolds for potential bone regeneration

Biomimetic scaffolds present the promising potential for bone regeneration. As a natural gel-like traditional food, tofu with porous architecture and proved biological safety indicated a good potential to be a natural scaffold and easy to be improved by surface modification. Hereon, we fabricated the tofu-based scaffolds and systematically explored the potential for bone tissue engineering. In addition, the collagen has been introduced by simple coating to further enhance the surface compatibility of the tofu-based scaffold in bone regeneration. The results showed that the tofu-based scaffolds possessed good porous structure and cytocompatibility. Notably, the tofu-based scaffolds could improve the expression of osteogenesis-related genes and proteins, leading to better bone regeneration after 2 months of implantation. All the results indicated that tofu would become an outstanding sustainable natural porous scaffold for bone regeneration with excellent bioactivities.     

Tofu as excellent scaffolds for potential bone regeneration

Biomimetic scaffolds present the promising potential for bone regeneration. As a natural gel-like traditional food, tofu with porous architecture and proved biological safety indicated a good potential to be a natural scaffold and easy to be improved by surface modification. Hereon, we fabricated the tofubased scaffolds and systematically explored the potential for bone tissue engineering. In addition, the collagen has been introduced by simple coating to further enhance the surface compatibility of the tofubased scaffold in bone regeneration. The results showed that the tofu-based scaffolds possessed good porous structure and cytocompatibility. Notably, the tofu-based scaffolds could improve the expression of osteogenesis-related genes and proteins, leading to better bone regeneration after 2 months of implantation. All the results indicated that tofu would become an outstanding sustainable natural porous scaffold for bone regeneration with excellent bioactivities.     

Synthesis of Functionalized Proline-Derived Azabicycloalkane Amino Acids and Their Applications in Drug Discovery: Recent Advances

After the first synthesis reported in 1994, azabicycloalkane amino acids have raised increasing interest, becoming one of the most important classes of constrained dipeptide mimics. Their incorporation into peptidomimetic structures allowed the obtainment of a wide range of biologically active compounds. Over the years, different research groups have worked at the development of synthetic strategies to gain these rigid dipeptide surrogates, nevertheless, methods affording functionalized and “easy-to-functionalize” derivatives are quite less described. The presence of a derivatizable azabicycloalkanone core could allow the introduction of chemical modifications aimed to improve the pharmaceutical properties of a biologically active compound without the need for redesigning its chemical synthesis. This account has collected and critically surveyed relevant approaches to the synthesis of functionalized azabicycloalkane amino acids, focusing the attention on the period of 2010 to the present. Moreover, recent applications of these compounds in drug discovery will be discussed.     

Recent advances in the asymmetric catalytic synthesis of chiral 3-hydroxy and 3-aminooxindoles and derivatives: Medicinally relevant compounds

Several oxindole derivatives, of natural or synthetic origin, have been identified as medicinally appealing compounds, with a plethora of bioactivities reported. Chiral 3-hydroxy and 3-aminooxindole scaffolds have captured the attention of several research groups, due to their importance in drug discovery. In this review, we systematically address the wide variety of asymmetric catalytic methodologies employed in the preparation of these relevant chiral scaffolds, present in many biologically active compounds and/or natural products. Special focus will be given to the nature of the catalyst used.     

Engineering mono- and multi-valent inhibitors on a modular scaffold

Here we exploit the simple, ultra-stable, modular architecture of consensus-designed tetratricopeptide repeat proteins (CTPRs) to create a platform capable of displaying both single as well as multiple functions and with diverse programmable geometrical arrangements by grafting non-helical short linear binding motifs (SLiMs) onto the loops between adjacent repeats. As proof of concept, we built synthetic CTPRs to bind and inhibit the human tankyrase proteins (hTNKS), which play a key role in Wnt signaling and are upregulated in cancer. A series of mono-valent and multi-valent hTNKS binders was assembled. To fully exploit the modular scaffold and to further diversify the multi-valent geometry, we engineered the binding modules with two different formats, one monomeric and the other trimeric. We show that the designed proteins are stable, correctly folded and capable of binding to and inhibiting the cellular activity of hTNKS leading to downregulation of the Wnt pathway. Multivalency in both the CTPR protein arrays and the hTNKS target results in the formation of large macromolecular assemblies, which can be visualized both in vitro and in the cell. When delivered into the cell by nanoparticle encapsulation, the multivalent CTPR proteins displayed exceptional activity. They are able to inhibit Wnt signaling where small molecule inhibitors have failed to date. Our results point to the tremendous potential of the CTPR platform to exploit a range of SLiMs and assemble synthetic binding molecules with built-in multivalent capabilities and precise, pre-programmed geometries.