Privileged substructures are of potentially great importance in medicinal chemistry. These scaffolds are characterized by their ability to promiscuously bind to a multitude of receptors through a variety of favorable characteristics. This may include presentation of their substituents in a spatially defined manner and perhaps also the ability to directly bind to the receptor itself, as well as exhibiting promising characteristics to aid bioavailability of the overall molecule. It is believed that some privileged substructures achieve this through the mimicry of common protein surface elements that are responsible for binding, such as β- and gamma;-turns. As a result, these structures represent a promising means by which new lead compounds may be identified.

The combinatorial synthesis of bicyclic privileged structures or privileged substructures

Modern drug discovery often involves screening small molecules for their ability to bind to a preselected protein target. Target-oriented syntheses of these small molecules, individually or as collections (focused libraries), can be planned effectively with retrosynthetic analysis. Drug discovery can also involve screening small molecules for their ability to modulate a biological pathway in cells or organisms, without regard for any particular protein target. This process is likely to benefit in the future from an evolving forward analysis of synthetic pathways, used in diversity-oriented synthesis, that leads to structurally complex and diverse small molecules. One goal of diversity-oriented syntheses is to synthesize efficiently a collection of small molecules capable of perturbing any disease-related biological pathway, leading eventually to the identification of therapeutic protein targets capable of being modulated by small molecules. Several synthetic planning principles for diversity-oriented synthesis and their role in the drug discovery process are presented in this review.

https://science.sciencemag.org/content/sci/287/5460/1964.full.pdf

Target-oriented and diversity-oriented organic synthesis in drug discovery.

http://www.chtf.stuba.sk/~szolcsanyi/education/files/Organicka%20chemia%20II/Prednaska%208_Aminokyseliny%20a%20peptidy/Doplnkove%20studijne%20materialy/Amide%20bond%20formation/Amide%20bond%20formation.pdf

Amide bond formation and peptide coupling

One of the initial steps in the development of therapeutic agents is the identification of lead compounds that bind to the receptor or enzyme target of interest. Many analogs of these lead compounds are then synthesized to define the key recognition elements for maximal activity. In general, many compounds must be evaluated in both the lead identification and optimization steps. Increasing burdens have been placed on these efforts due to the large number of new therapeutic targets that continue to be identified thorough modern molecular biology methods.1 To address this demand, very powerful chemical and biological methods have been developed for the generation of large combinatorial libraries of peptides2 and oligonucleotides3 that are then screened against a receptor or enzyme to identify high-affinity ligands or potent inhibitors, respectively. While these studies have clearly demonstrated the power of library synthesis and screening strategies, peptides and oligonucleotides generally have poor oral activities and rapid in vivo clearance;4 therefore their utility as bioavailable therapeutic agents is often limited. Due to the favorable pharmacokinetic properties of many small organic molecules (<600-700 molecular weight),5 the design, synthesis, and evaluation of libraries of these compounds6 has rapidly become a major frontier in organic chemistry. Lorin A. Thompson was born in Lexington, KY, in 1970. He received the Bachelor of Science degree from the University of North Carolina, Chapel Hill, in 1992 where he worked under the guidance of Joseph Desimone. He is currently pursuing his doctorate in the laboratory of Jonathan Ellman at UC Berkeley where he is the 1994 Glaxo-Wellcome fellow. His research interests include the development of synthetic methodology for organic library construction.

/pdf/synthesis-and-applications-of-small-molecule-libraries-3n3gol8dyk.pdf

Synthesis and Applications of Small Molecule Libraries.

Privileged Scaffolds for Library Design and Drug Discovery

We describe a file format that is designed to represent mixtures of compounds in a way that is fully machine readable. This Mixfile format is intended to fill the same role for substances that are composed of multiple components as the venerable Molfile does for specifying individual structures. This much needed datastructure is intended to replace current practices for communicating information about mixtures, which usually relies on human-readable text descriptions, drawing several species within a single molecular diagram, or mutually incompatible ad hoc solutions. We describe an open source software application for editing mixture files, which can also be used as web-ready tools for manipulating the file format. We also present a corpus of mixture examples, which we have extracted from collections of text-based descriptions. Furthermore, we present an early look at the proposed IUPAC Mixtures InChI specification, instances of which can be automatically generated using the Mixfile format as a precursor.

/pdf/capturing-mixture-composition-an-open-machine-readable-2703jcsy9i.pdf

Capturing mixture composition: an open machine-readable format for representing mixed substances

Alternative business models for drug discovery.

Collaborative drug discovery for More Medicines for Tuberculosis (MM4TB).

Compounds containing the tetrahydroisoquinoline ring system were prepared using solid-supported ester derivatives on a nucleophile-sensitive resin, starting from the corresponding BOC-protected amino acids. The key heterocyclic intermediates were obtained from the Pictet−Spengler reaction between ethyl glyoxylate or methyl 4-formylbenzoate and dopamine or 3-hydroxyphenethylamine. After the resulting amino esters were converted to the BOC derivatives, the phenolic hydroxyl groups were alkylated with a series of alkyl halides to afford the corresponding ethers. Ester hydrolysis afforded the BOC-protected tetrahydroisoquinoline carboxylic acid scaffolds, which were then attached to (4-hydroxyphenyl)sulfide resin (Marshall linker) as the corresponding ester. The BOC group was removed under acidic conditions, and the resulting support-bound amine hydrochlorides were converted to the corresponding amides using a set of carboxylic acids. The support-bound amides were liberated with amines to produce the desired ...

Barry A. Bunin

Papers

Capturing mixture composition: an open machine-readable format for representing mixed substances

Alternative business models for drug discovery.

Collaborative drug discovery for More Medicines for Tuberculosis (MM4TB).

Solid-phase synthesis of 1-substituted tetrahydroisoquinoline derivatives employing BOC-protected tetrahydroisoquinoline carboxylic acids.

Increasing the efficiency of small-molecule drug discovery.