Emerging chemical and biological approaches for the preparation of discovery libraries

Building Natural Product Libraries Using Quantitative Clade-Based and Chemical Clustering Strategies

The success of natural product-based drug discovery is predicated on having chemical collections that offer broad coverage of metabolite diversity. We propose a simple set of tools combining genetic barcoding and metabolomics to help investigators build natural product libraries aimed at achieving predetermined levels of chemical coverage. It was found that such tools aided in identifying overlooked pockets of chemical diversity within taxa, which could be useful for refocusing collection strategies. We have used fungal isolates identified as Alternaria from a citizen-science-based soil collection to demonstrate the application of these tools for assessing and carrying out predictive measurements of chemical diversity in a natural product collection. Within Alternaria, different subclades were found to contain nonequivalent levels of chemical diversity. It was also determined that a surprisingly modest number of isolates (195 isolates) was sufficient to afford nearly 99% of Alternaria chemical features in the data set. However, this result must be considered in the context that 17.9% of chemical features appeared in single isolates, suggesting that fungi like Alternaria might be engaged in an ongoing process of actively exploring nature's metabolic landscape. Our results demonstrate that combining modest investments in securing internal transcribed spacer (ITS)-based sequence information (i.e., establishing gene-based clades) with data from liquid chromatography-mass spectrometry (i.e., generating feature accumulation curves) offers a useful route to obtaining actionable insights into chemical diversity coverage trends in a natural product library. It is anticipated that these outcomes could be used to improve opportunities for accessing bioactive molecules that serve as the cornerstone of natural product-based drug discovery. IMPORTANCE Natural product drug discovery efforts rely on libraries of organisms to provide access to diverse pools of compounds. Actionable strategies to rationally maximize chemical diversity, rather than relying on serendipity, can add value to such efforts. Readily implementable biological (i.e., ITS sequence analysis) and chemical (i.e., mass spectrometry-based feature and scaffold measurements) diversity assessment tools can be employed to monitor and adjust library development tactics in real time. In summary, metabolomics-driven technologies and simple gene-based specimen barcoding approaches have broad applicability to building chemically diverse natural product libraries.

Calcium Oscillation Frequency Is a Potential Functional Complex Physiological Relevance Indicator for a Neuroblastoma-Based 3D Culture Model

In vitro screening for drugs that affect neural function in vivo is still primitive. It primarily relies on single cellular responses from 2D monolayer cultures that have been shown to be exaggerations of the in vivo response. For the 3D model to be physiologically relevant, it should express characteristics that not only differentiate it from 2D but also closely emulate those seen in vivo. These complex physiologically relevant (CPR) outcomes can serve as a standard for determining how close a 3D culture is to its native tissue or which out of a given number of 3D platforms is better suited for a given application. In this study, Fluo-4-based calcium fluorescence imaging was performed followed by automated image data processing to quantify the calcium oscillation frequency of SHSY5Y cells cultured in 2D and 3D formats. It was found that the calcium oscillation frequency is upregulated in traditional 2D cultures while it was comparable to in vivo in spheroid and microporous polymer scaffold-based 3D models, suggesting calcium oscillation frequency as a potential functional CPR indicator for neural cultures.

Intracellular Production of Cyclic Peptide Libraries with SICLOPPS

Cyclic peptides are an important class of molecules that are increasingly viewed as an ideal scaffold for inhibition of protein-protein interactions (PPI). Here we detail an approach that enables the intracellular synthesis of cyclic peptide libraries of around 10⁸ members. The method utilizes split intein mediated circular ligation of peptides and proteins (SICLOPPS), taking advantage of split intein splicing to cyclize a library of peptide sequences. SICLOPPS allows the ring size, set residues and number of random residues within a library to be predetermined by the user. SICLOPPS libraries have been combined with a variety of cell-based screens to identify cyclic peptide inhibitors of a variety of enzymes and protein-protein interactions.

Docking methods for structure-based library design

The drug discovery process mainly relies on the experimental high-throughput screening of huge compound libraries in their pursuit of new active compounds. However, spiraling research and development costs and unimpressive success rates have driven the development of more rational, efficient, and cost-effective methods. With the increasing availability of protein structural information, advancement in computational algorithms, and faster computing resources, in silico docking-based methods are increasingly used to design smaller and focused compound libraries in order to reduce screening efforts and costs and at the same time identify active compounds with a better chance of progressing through the optimization stages. This chapter is a primer on the various docking-based methods developed for the purpose of structure-based library design. Our aim is to elucidate some basic terms related to the docking technique and explain the methodology behind several docking-based library design methods. This chapter also aims to guide the novice computational practitioner by laying out the general steps involved for such an exercise. Selected successful case studies conclude this chapter.

Intein-mediated cyclization of randomized peptides in the periplasm of Escherichia coli and their extracellular secretion

Split-inteins can be used to generate backbone cyclized peptide as a source of new bioactive molecules. In this work we show that cysteine-mediated splicing can be performed in the oxidative environment of the periplasm of Escherichia coli. Cyclization of the TEM-1 beta-lactamase and of small randomized peptides was demonstrated using an artificially permuted version of the DnaB mini-intein from Synechocystis sp. PCC6803 strain fused to a signal sequence. For small peptides, a signal sequence that promotes cotranslational translocation had to be used. Efficient backbone cyclization was observed for more than 50% of combinatorial peptides featuring a fully randomized sequence inserted between a serine and glycine that are necessary for fast splicing. Furthermore, by coexpressing a mutant of the pIV outer membrane pore protein of fd bacteriophage, we showed that peptides can diffuse in the extracellular medium. These results open new routes for searching compounds acting on new targets such as exported and membrane proteins or pathogen microorganisms.

Application of natural product-inspired diversity-oriented synthesis to drug discovery

Natural products have played a critical role in the identification of numerous medicines. Synthetic organic chemistry and combinatorial chemistry strategies such as diversity-oriented synthesis (DOS) have enabled the synthesis of natural product-like compounds. The combination of these approaches has both improved the desired biological properties of natural products as well as the identification of novel compounds. Diversity concepts and strategies to access novel compounds inspired by natural products will be reviewed.

Split-intein mediated circular ligation used in the synthesis of cyclic peptide libraries in E. coli

Recent advances in chemical biology and the advantages presented by in vivo screening have highlighted the need for a robust and flexible biologically synthesized small-molecule library. Herein we describe a method for the biosynthesis of cyclic peptide libraries of up to 10(8) members in Escherichia coli using split-intein circular ligation of peptides and proteins (SICLOPPS). The method utilizes split-intein chemistry to cyclize randomized peptide sequences. The cyclic peptide library can potentially be of any size and the peptide itself may contain unlimited random residues. However, the library size is limited by the transformation efficiency of E. coli and random residues are generally limited to five, but additional amino acids can be used in the cyclic peptide backbone, varying the structure and ring size of the cyclic peptide. SICLOPPS libraries have been combined with a bacterial reverse two-hybrid system in our labs and used in the identification of inhibitors of several protein-protein interactions. This protocol is expected to take around 3-4 weeks to implement.

Improving the universal response of evaporative light scattering detection by mobile phase compensation

Mobile phase compensation, first reported for the charged aerosol detector (CAD), was used as a suitable method to overcome problems related to the mobile phase-dependent response of the evaporative light scattering detector (ELSD). Mobile phase compensation was effectively performed both in the flow injection- and in gradient modes. Without compensation, the response factors of the ELSD for six sulfonamide drugs differed by a factor of two when varying the mobile phase composition between 10 and 90% acetonitrile. This change could be effectively eliminated using the technique of mobile phase compensation, where a secondary pump with a reversed gradient was used to provide the detector with a constant composition of the mobile phase. For identical experimental conditions, the ELSD showed a nearly constant, albeit somewhat reduced, response with compensation. This indicates that under such conditions, the ELSD behaved as a concentration-sensitive detector. The analysis of sulfonamides drugs at 0.05% level using gradient UPLC-ELSD separation with mobile phase compensation is demonstrated.

Antibody engineering and modification technologies

Antibody engineering has become a well-developed discipline, encompassing discovery methods, production strategies, and modification techniques that have brought forth clinically investigated and marketed therapeutics. The realization of the long-standing goal of production of fully human monoclonal antibodies has focused intensive research on the clinical employment of this potent drug category. However, antibodies are large macromolecules that pose numerous challenges in formulation, optimal pharmacokinetics, manufacturing, stability, and process development. While further improvements in discovery technologies, such as phage display, ribosome display, and transgenic animals continue to advance our capacity to rapidly screen and refine optimal binding molecules, antibody engineers have recently focused more of their efforts on improving protein production and stability, as well as engineering improved biological properties in the effector domains of monoclonal antibodies. A second long-standing goal of antibody engineering, the development of targeted drugs, has not been wholly realized, but this obvious application for antibodies is currently undergoing increasing exploration. Minimal binding proteins, such as Fab, scFv, and single variable domains are the preferred targeting elements for some investigational drugs, whereas non-immunoglobulin scaffold proteins have been explored as binding proteins in other designs. The necessity to utilize non-protein components in targeted drugs, such as polymers, linkers, and cytotoxics, has brought a convergence of the fields of bioconjugate chemistry and protein engineering in experimental antibody therapeutics.