Construction Of Combinatorial Libraries Research Articles

A VersaTile-driven platform for rapid hit-to-lead development of engineered lysins.

Health care authorities are calling for new antibacterial therapies to cope with the global emergence of antibiotic-resistant bacteria. Bacteriophage-encoded lysins are a unique class of antibacterials with promising (pre)clinical progress. Custom engineering of lysins allows for the creation of variants against potentially any bacterial pathogen. We here present a high-throughput hit-to-lead development platform for engineered lysins. The platform is driven by VersaTile, a new DNA assembly method for the rapid construction of combinatorial libraries of engineered lysins. We constructed approximately 10,000 lysin variants. Using an iterative screening procedure, we identified a lead variant with high antibacterial activity against Acinetobacter baumannii in human serum and an ex vivo pig burn wound model. This generic platform could offer new opportunities to populate the preclinical pipeline with engineered lysins for diverse (therapeutic) applications.

Convenient synthesis of 2-(4-amino-1H-1,2,3-triazol-1-yl) acetic acid

A convenient approach to the synthesis of 2-(4-amino-1 H -1,2,3-triazol-1-yl) acetic acid is shown, that may be general for the synthesis of 4-amino-1 H -1,2,3-triazole carboxylic acid analogues and peptide compounds based on them. As a convenient starting agent, we selected 2-azido-N,N-diethylacetamide, which is readily obtained from the corresponding chloroacetamide and is a stable solid substance. Azide reacts with a methyl propiolate in the presence of a catalytic amount of CuI and triethylamine as a co-catalyst, occurs in high yields and leads to the formation of triazole. The presence of an amide and ester group in the molecule opens the possibility of their selective modification. In addition, it should be noted that the electronegative triazole ring promotes the hydrolysis of the ester group at position 4 intriazole. Thus, by performing the hydrolysis of the ester under mild conditions at room temperature, acid was obtained selectively with a yield close to the quantitative one. Nevertheless, acetamide fragment was not hydrolyzed. The action on acid with oxalyl chloride is quantitatively converted to acyl chloride. The last one easily undergoes aminolysis to form amide and also interacts with sodium azide to form azide. Amide is promising for further studies, in particular as a precursor of the nitrile group. Azide was found to be a stable crystalline at room temperature, was isolated and characterized by 1 H NMR spectroscopy. In the conditions of the Curtius rearrangement, azide was converted to the corresponding tert-butyl carbamate, which is a convenient precursor of the amino acid. The target amino acid was obtained with a good yield after removal of tert-butyl carbamate protection group with trifluoroacetic acid followed by hydrolysis of amide when heated in 10 % NaOH. An example of the synthesis of 2-(4-amino-1 H -1,2,3-triazol-1-yl)acetic acid demonstrates a convenient way of selective modification of the substituents in the triazole, which open prospects for the preparation of isostructural derivatives and the construction of combinatorial libraries of peptidomimetics to find biologically active compounds. Keywords : azides, 1,3-dipolar cycloaddition, 1,2,3-triazoles, amino acids, peptidomimetics.

Yeast Surface Display and Cell Sorting of Antigen-Binding Fc Fragments.

Since the introduction of the yeast display platform, this method has increasingly gained popularity for the discovery and affinity maturation of antibodies and other protein scaffolds intended for antigen recognition. Yeast display is particularly well suited for the selection of antigen-binding Fc fragments (Fcabs) as it allows rapid combinatorial library construction via gap repair-driven homologous recombination and an efficient display of a glycosylated Fc able to interact with Fcγ receptors. Apart from expression-related normalization, isolation of properly folded Fcabs can be guided efficiently by simultaneous staining with ligands such as protein A, FcγRI, or the conformation-sensitive anti-FigCH2 antibody, whose binding is critically dependent on the integrity of the Fc structure. The particular properties of the Fcab scaffold, such as its homodimeric state which can promote binding to multiple antigen molecules, require modifications of traditional affinity maturation strategies. Preferred to equilibrium selections are kinetically driven antigen selections, designed to specifically influence the binding off-rate, which in many cases augments the desired biological effect. A simple design of a yeast-displayed heterodimeric Fc fragment is described and can be used as a general guideline for affinity selection of Fcabs with an asymmetric binding site. Overall, this chapter underlines the importance of the versatile yeast display technique for the optimization of the novel Fcab scaffold for antigen recognition.

Start-Stop Assembly: a functionally scarless DNA assembly system optimized for metabolic engineering.

DNA assembly allows individual DNA constructs or libraries to be assembled quickly and reliably. Most methods are either: (i) Modular, easily scalable and suitable for combinatorial assembly, but leave undesirable ‘scar’ sequences; or (ii) bespoke (non-modular), scarless but less suitable for construction of combinatorial libraries. Both have limitations for metabolic engineering. To overcome this trade-off we devised Start-Stop Assembly, a multi-part, modular DNA assembly method which is both functionally scarless and suitable for combinatorial assembly. Crucially, 3 bp overhangs corresponding to start and stop codons are used to assemble coding sequences into expression units, avoiding scars at sensitive coding sequence boundaries. Building on this concept, a complete DNA assembly framework was designed and implemented, allowing assembly of up to 15 genes from up to 60 parts (or mixtures); monocistronic, operon-based or hybrid configurations; and a new streamlined assembly hierarchy minimizing the number of vectors. Only one destination vector is required per organism, reflecting our optimization of the system for metabolic engineering in diverse organisms. Metabolic engineering using Start-Stop Assembly was demonstrated by combinatorial assembly of carotenoid pathways in Escherichia coli resulting in a wide range of carotenoid production and colony size phenotypes indicating the intended exploration of design space.

Front Cover: Beating Bias in the Directed Evolution of Proteins: Combining High‐Fidelity on‐Chip Solid‐Phase Gene Synthesis with Efficient Gene Assembly for Combinatorial Library Construction (ChemBioChem 3/2018)

Front Cover: Beating Bias in the Directed Evolution of Proteins: Combining High‐Fidelity on‐Chip Solid‐Phase Gene Synthesis with Efficient Gene Assembly for Combinatorial Library Construction (ChemBioChem 3/2018)

Beating Bias in the Directed Evolution of Proteins: Combining High-Fidelity on-Chip Solid-Phase Gene Synthesis with Efficient Gene Assembly for Combinatorial Library Construction.

Saturation mutagenesis (SM) constitutes a widely used technique in the directed evolution of selective enzymes as catalysts in organic chemistry and in the manipulation of metabolic paths and genomes, but the quality of the libraries is far from optimal due to the inherent amino acid bias. Herein, it is shown how this fundamental problem can be solved by applying high-fidelity solid-phase chemical gene synthesis on silicon chips followed by efficient gene assembly. Limonene epoxide hydrolase was chosen as the catalyst in the model desymmetrization of cyclohexene oxide with the stereoselective formation of (R,R)- and (S,S)-cyclohexane-1,2-diol. A traditional combinatorial PCR-based SM library, produced by simultaneous randomization at several residues by using a reduced amino acid alphabet, and the respective synthetic library were constructed and compared. Statistical analysis at the DNA level with massive sequencing demonstrates that, in the synthetic approach, 97 % of the theoretically possible DNA mutants are formed, whereas the traditional SM library contained only about 50 %. Screening at the protein level also showed the superiority of the synthetic library; many highly (R,R)- and (S,S)-selective variants being discovered are not found in the traditional SM library. With the prices of synthetic genes decreasing, this approach may point the way to future directed evolution.

Combinatorial Library Based on Restriction Enzyme-mediated Modular Assembly.

Combinatorial approaches in directed evolution were proven to be more efficient for exploring sequence space and innovating function of protein. Here, we presented the modular assembly of secondary structures (MASS) for constructing a combinatorial library. In this approach, secondary structure elements were extracted from natural existing protein. The common linkers were flanking secondary structure elements, and then secondary structure elements were digested by Hinf I restriction endonuclease that was used in the construction of combinatorial library for the first time. The digested DNA fragments were randomly ligated in the sense orientation, then in sequence to be amplified by PCR and transformation. This approach showed that different DNA fragments without homologous sequences could be randomly assembled to create significant sequence space. With the structure analysis of recombinants, it would be beneficial to the rational design, even to the design of protein de novo, and to evolve any genetic part or circuit.

Using Hierarchical Virtual Screening To Combat Drug Resistance of the HIV-1 Protease.

Human immunodeficiency virus (HIV) protease inhibitors (PIs) are important components of highly active anti-retroviral therapy (HAART) that block the catalytic site of HIV protease, thus preventing maturation of the HIV virion. However, with two decades of PI prescriptions in clinical practice, drug-resistant HIV mutants have now been found for all of the PI drugs. Therefore, the continuous development of new PI drugs is crucial both to combat the existing drug-resistant HIV strains and to provide treatments for future patients. Here we purpose an HIV PI drug design strategy to select candidate PIs with binding energy distributions dominated by interactions with conserved protease residues in both wild-type and various drug-resistant mutants. On the basis of this strategy, we have constructed a virtual screening pipeline including combinatorial library construction, combinatorial docking, MM/GBSA-based rescoring, and reranking on the basis of the binding energy distribution. We have tested our strategy on lopinavir by modifying its two functional groups. From an initial 751 689 candidate molecules, 18 candidate inhibitors were selected using the pipeline for experimental validation. IC50 measurements and drug resistance predictions successfully identified two ligands with both HIV protease inhibitor activity and an improved drug resistance profile on 2382 HIV mutants. This study provides a proof of concept for the integration of MM/GBSA energy analysis and drug resistance information at the stage of virtual screening and sheds light on future HIV drug design and the use of virtual screening to combat drug resistance.

Sulfate Encapsulation in Supramolecular Structures from L‐Asparagine‐Derived 2,5‐Diketopiperazine Scaffolds: Anion Binding

AbstractWe report a new sulfate receptor, anchored onto 2,5‐diketopiperazine units, which results in the formation of two types of supramolecules; one in which the sulfate ion guest fits snugly into extended cavities and the other in which the guest is sandwiched between layers. In each case, the anion is held by six hydrogen bonds from the host. 1H NMR spectroscopic solution studies enabled the construction of Job plots, and calculation of stoichiometry and association constants. These findings are of possible significance in drug design and for construction of combinatorial libraries.

Heuristic for maximizing DNA reuse in synthetic DNA library assembly.

De novo DNA synthesis is in need of new ideas for increasing production rate and reducing cost. DNA reuse in combinatorial library construction is one such idea. Here, we describe an algorithm for planning multistage assembly of DNA libraries with shared intermediates that greedily attempts to maximize DNA reuse, and show both theoretically and empirically that it runs in linear time. We compare solution quality and algorithmic performance to the best results reported for computing DNA assembly graphs, finding that our algorithm achieves solutions of equivalent quality but with dramatically shorter running times and substantially improved scalability. We also show that the related computational problem bounded-depth min-cost string production (BDMSP), which captures DNA library assembly operations with a simplified cost model, is NP-hard and APX-hard by reduction from vertex cover. The algorithm presented here provides solutions of near-minimal stages and thanks to almost instantaneous planning of DNA libraries it can be used as a metric of "manufacturability" to guide DNA library design. Rapid planning remains applicable even for DNA library sizes vastly exceeding today's biochemical assembly methods, future-proofing our method.

4-Aminocyclopentane-1,3-diols as Platforms for Diversity: Synthesis of Anandamide Analogs

Starting from cyclopentadiene, two racemic mixtures of 4-aminocyclopentane-1,3-diols were prepared in 8 steps and characterized. Structure determination proved the anticipated trans-orientation of the two oxygen atoms with respect to the plane of the ring. The fragment-like new compounds are small and hydrophilic, devoid of rotatable bonds, and offer stereochemically defined attachment points for substituents. Thus, these platforms for diversity are suitable starting points for the construction of combinatorial libraries of lead-like 4-amidocyclopentane-1,3-diols or natural product analogs. As a proof of concept, cyclopentanoid anandamide analogs were prepared using these molecular platforms and evaluated as tools for the investigation of unresolved issues in the molecular biology of anandamide.

Sequential Coupling Approach to the Synthesis of Nickel(II) Complexes with N-aryl-2-amino Phenolates

A sequential multicomponent coupling approach is a powerful method for the construction of combinatorial libraries because structurally complex and diverse molecules can be synthesized from simple materials in short steps. In this paper, an efficient synthesis of nickel(II) complexes with N-aryl-2-amino phenols via a sequential three-step coupling approach is described, for potential use in nonlinear optical materials, bioinspired catalytic systems, and near-infrared absorbing filters. Seventeen N-aryl-2-amino phenolates were successfully synthesized in high yields based on the coupling of 3,5-di-tert-butylbenzene-1,2-diol with a pivotal aromatic scaffold, 4-bromo-2-iodo-aniline, followed by sequential Suzuki-Miyaura coupling with aryl boronates. A total of 16 analytically pure nickel(II) complexes with N-aryl-2-amino phenolates were obtained from 17 complexation trials. The procedure allowed us to assemble 4 components in high yields without protection, deprotection, oxidation or reduction steps. Various building blocks that included electron-donating, electron-withdrawing, and basic were used, and readily available, nontoxic and environmentally benign substrates and reagents were employed with no generation of toxic compounds. No strict anhydrous or degassed conditions were required. Absorption spectroscopic measurement of the synthesized nickel(II) complexes revealed that the ortho-substituent Ar(1) exerted more influence on the absorption wavelength of the complexes than the para-substituent Ar(2). On the other hand, both substituents Ar(1) and Ar(2) influenced the molar absorptivity values. These observations should be useful for the design of new and useful nickel(II) complexes as near-infrared chromophores.

Scaffold Diversification Enhances Effectiveness of a Superlibrary of Hyperthermophilic Proteins

The use of binding proteins from non-immunoglobulin scaffolds has become increasingly common in biotechnology and medicine. Typically, binders are isolated from a combinatorial library generated by mutating a single scaffold protein. In contrast, here we generated a "superlibrary" or "library-of-libraries" of 4 × 10(8) protein variants by mutagenesis of seven different hyperthermophilic proteins; six of the seven proteins have not been used as scaffolds prior to this study. Binding proteins for five different model targets were successfully isolated from this library. Binders obtained were derived from five out of the seven scaffolds. Strikingly, binders from this modestly sized superlibrary have affinities comparable or higher than those obtained from a library with 1000-fold higher sequence diversity but derived from a single stable scaffold. Thus scaffold diversification, i.e., randomization of multiple different scaffolds, is a powerful alternate strategy for combinatorial library construction.

Profile of Keith Joung

Profile of Keith Joung

Digestion-after-shuffling: A method for combinatorial library construction

We have developed a convenient method for family shuffling of amino acid sequences, termed digestion-after-shuffling. After DNA shuffling of homologous genes, plasmid mixture is extracted from a library and used for several double digestions with restriction enzymes. For each double digestion, two restriction enzymes are selected, corresponding to the single restriction sites of different parental genes. After digestions, fragments with expected sizes are obtained by gel purification and religated to construct recombinant plasmids. Thus, the obtained genes should be chimeras and have at least two restriction sites originating from different parental sequences.

Organic Virtual Library (ORVIL) - A Combinatorial Library Construction based on Organic Constituents and without Scaffold Hopping

Rapid construction of virtual combinatorial library is a prerequisite for in silico library enumeration and design. Organic Virtual Library (ORVIL) is a perl programme to generate a combinatorial library using most frequently observed 200 organic substituents. It is designed to explore the organic chemical space in the given query structure without affecting the entire backbone of the molecule enabling minimum molecular complexities. Its particular features are its simplicity to use, portable SMILES format and high speed of library construction. Benchmarking of Tamoxifen (drug for breast cancer) was performed which revealed a compound having similar architecture of known drug analogue, Toremifene.

ChemInform Abstract: Organocatalyzed Enantioselective One‐Pot Three‐Component Access to Indoloquinolizidines by a Michael Addition—Pictet—Spengler Sequence.

AbstractThe title method is potentially useful in combinatorial library construction and the synthesis of natural alkaloids.

Selectively N‐Protected Enantiopure 2,5‐Disubstituted Piperazines: Avoiding the Pitfalls in Solid‐Phase Fukuyama–Mitsunobu Cyclizations

An efficient solid-phase route to ring-substituted piperazines from O-linked resin-bound (S)-aziridine-2-methanol is described. Regioselective microwave-assisted aminolysis followed by intramolecular Fukuyama-Mitsunobu cyclization constitute the key features of the protocol. Simple piperazines and diazepanes were readily obtained without preceding N-protection of the acyclic intermediate, whereas attempts to extend this protocol to chiral 2,5-disubstituted piperazines failed. Modifications encompassing N-carbamoylation prior to ring-closure were therefore investigated. However, standard carbamoylating agents, for example, Fmoc-Cl and Alloc-Cl tended to give bis-protected by-products. Thus, novel microwave-assisted solid-phase N-protection procedures were developed for efficient introduction of Fmoc, Boc and Alloc groups. The subsequent cyclization proceeded in moderate to excellent yields depending on the bulk of the side chain and type of N-protecting group. This protocol readily provided novel cis- and trans-2,5-disubstituted piperazines displaying a variety of N-protecting group patterns after further on-resin manipulations. Also, unexpected by-products obtained during these optimization studies were identified and characterized. This includes nosylated ureas arising from an alternative cyclization pathway. Finally, post-cleavage oxidation gave access to the Fmoc/Boc-protected alpha-amino acid as well as the corresponding aldehyde. The chiral piperazines described in this work will enable construction of combinatorial libraries with a higher chemical diversity compared to those containing simple N,N'-difunctionalized piperazines, often present in drug-like compounds.

Sequential Cu(I)/Pd(0)-catalyzed multicomponent coupling and annulation protocol for the synthesis of indenoisoquinolines.

Copper-catalyzed coupling of imines, vinylstannanes, or alkynes and o-bromoaroyl chlorides followed by Pd(0)-catalyzed annulations afforded indenoisoquinolines. Protocols requiring minimal purifications were developed, providing new methods for the construction of combinatorial libraries.

A Practical Synthesis of Differentially Protected 2-(Hydroxymethyl)piperazines

An efficient and scalable synthesis of three differentially protected 2-(hydroxymethyl)piperazines is presented, starting from optically active and commercially available (2S)-piperazine-2-carboxylic acid dihydrochloride. These synthetic building blocks are useful in the preparation of biologically active compounds and as chemical scaffolds for the construction of combinatorial libraries.