Quick Building Blocks (QBB): An Innovative and Efficient Business Model To Speed Medicinal Chemistry Analog Synthesis

Building Block-Centric Approach to DNA-Encoded Library Design

DNA-encoded library technology grants access to nearly infinite opportunities to explore the chemical structure space for drug discovery. Successful navigation depends on the design and synthesis of libraries with appropriate physicochemical properties (PCPs) and structural diversity while aligning with practical considerations. To this end, we analyze combinatorial library design constraints including the number of chemistry cycles, bond construction strategies, and building block (BB) class selection in pursuit of ideal library designs. We compare two-cycle library designs (amino acid + carboxylic acid, primary amine + carboxylic acid) in the context of PCPs and chemical space coverage, given different BB selection strategies and constraints. We find that broad availability of amines and acids is essential for enabling the widest exploration of chemical space. Surprisingly, cost is not a driving factor, and virtually, the same chemical space can be explored with "budget" BBs.

Exploring the combinatorial explosion of amine-acid reaction space via graph editing

Amines and carboxylic acids are abundant chemical feedstocks that are nearly exclusively united via the amide coupling reaction. The disproportionate use of the amide coupling leaves a large section of unexplored reaction space between amines and acids: two of the most common chemical building blocks. Herein we conduct a thorough exploration of amine-acid reaction space via systematic enumeration of reactions involving a simple amine-carboxylic acid pair. This approach to chemical space exploration investigates the coarse and fine modulation of physicochemical properties and molecular shapes. With the invention of reaction methods becoming increasingly automated and bringing conceptual reactions into reality, our map provides an entirely new axis of chemical space exploration for rational property design.

Identification of parallel medicinal chemistry protocols to expand branched amine design space

α-Branched heteroaryl amines are prevalent motifs in drugs and are typically prepared through C-N bond formation. In contrast, C-C bond-forming approaches to branched amines may dramatically expand available chemical space but are rarely pursued in parallel format due to a lack of established library protocols. Methods for the synthesis of α-branched heteroaryl amines via aldimine addition have been evaluated for compatibility with parallel synthesis. In situ activation of aliphatic carboxylic acids as redox-active esters enables Zn-mediated decarboxylative radical imine addition to access aliphatic-branched heterobenzylic amines. In situ activation of (hetero)aryl bromides via Li-halogen exchange enables heteroaryl-lithium addition to imines to access (hetero)benzhydryl amines. Condensation of heteroaryl amines with heteroaryl aldehydes provides aldimines which may be intercepted with aryl Grignard reagents to provide modular access to (hetero)benzhydryl amines. These protocols minimize synthetic step count and maximize accessible design space, enhancing access to α-branched heteroaryl amines for medicinal chemistry.

Decarbonylative Pd-Catalyzed Suzuki Cross-Coupling for the Synthesis of Structurally Diverse Heterobiaryls

Heteroaromatic biaryls are core scaffolds found in a plethora of pharmaceuticals; however, their direct synthesis by the Suzuki cross-coupling is limited to heteroaromatic halide starting materials. Here, we report a direct synthesis of diverse nitrogen-containing heteroaromatic biaryls by Pd-catalyzed decarbonylative Suzuki cross-coupling of widely available heterocyclic carboxylic acids with arylboronic acids. The practical and modular nature of this cross-coupling enabled the straightforward preparation of >45 heterobiaryl products using pyridines, pyrimidines, pyrazines, and quinolines in excellent yields. We anticipate that the modular nature of this protocol will find broad application in medicinal chemistry and drug discovery research.

A Close-up Look at the Chemical Space of Commercially Available Building Blocks for Medicinal Chemistry

The ability to efficiently synthesize desired compounds can be a limiting factor for chemical space exploration in drug discovery. This ability is conditioned not only by the existence of well-studied synthetic protocols but also by the availability of corresponding reagents, so-called building blocks (BBs). In this work, we present a detailed analysis of the chemical space of 400 000 purchasable BBs. The chemical space was defined by corresponding synthons─fragments contributed to the final molecules upon reaction. They allow an analysis of BB physicochemical properties and diversity, unbiased by the leaving and protective groups in actual reagents. The main classes of BBs were analyzed in terms of their availability, rule-of-two-defined quality, and diversity. Available BBs were eventually compared to a reference set of biologically relevant synthons derived from ChEMBL fragmentation, in order to illustrate how well they cover the actual medicinal chemistry needs. This was performed on a newly constructed universal generative topographic map of synthon chemical space that enables visualization of both libraries and analysis of their overlapped and library-specific regions.

What is in Our Kit? An Analysis of Building Blocks Used in Medicinal Chemistry Parallel Libraries

Building blocks are the molecular foundations for drug molecule design. The building block is one of the determining factors of final compound qualities in any given medicinal chemistry campaign. Herein, we describe our analysis of the building blocks used in parallel library synthesis at AbbVie. The results gave insights into the synthetic tractability and accessibilities of building blocks used in medicinal chemistry. Furthermore, our analysis showed that opportunities still exist for the identification and future incorporation of underrepresented building blocks, even for commonly used reactions, to obtain intellectual and competitive advantages in drug discovery.

The Formal Cross-Coupling of Amines and Carboxylic Acids to Form sp3 -sp3 Carbon-Carbon Bonds

We have developed a deaminative-decarboxylative protocol to form new carbon(sp³ )-carbon(sp³ ) bonds from activated amines and carboxylic acids. Amines and carboxylic acids are ubiquitous building blocks, available in broad chemical diversity and at lower cost than typical C-C coupling partners. To leverage amines and acids for C-C coupling, we developed a reductive nickel-catalyzed cross-coupling utilizing building block activation as pyridinium salts and redox-active esters, respectively. Miniaturized high-throughput experimentation studies were critical to our reaction optimization, with subtle experimental changes such as order of reagent addition, composition of a binary solvent system, and ligand identity having a significant impact on reaction performance. The developed protocol is used in the late-stage diversification of pharmaceuticals while more than one thousand systematically captured and machine-readable reaction datapoints are reposited.

DNA-Encoded Chemistry: Drug Discovery from a Few Good Reactions

Click chemistry, proposed nearly 20 years ago, promised access to novel chemical space by empowering combinatorial library synthesis with a "few good reactions". These click reactions fulfilled key criteria (broad scope, quantitative yield, abundant starting material, mild reaction conditions, and high chemoselectivity), keeping the focus on molecules that would be easy to make, yet structurally diverse. This philosophy bears a striking resemblance to DNA-encoded library (DEL) technology, the now-dominant combinatorial chemistry paradigm. This review highlights the similarities between click and DEL reaction design and deployment in combinatorial library settings, providing a framework for the design of new DEL synthesis technologies to enable next-generation drug discovery.

Fragment-based drug discovery: opportunities for organic synthesis

This Review describes the increasing demand for organic synthesis to facilitate fragment-based drug discovery (FBDD), focusing on polar, unprotected fragments. In FBDD, X-ray crystal structures are used to design target molecules for synthesis with new groups added onto a fragment via specific growth vectors. This requires challenging synthesis which slows down drug discovery, and some fragments are not progressed into optimisation due to synthetic intractability. We have evaluated the output from Astex's fragment screenings for a number of programs, including urokinase-type plasminogen activator, hematopoietic prostaglandin D2 synthase, and hepatitis C virus NS3 protease-helicase, and identified fragments that were not elaborated due, in part, to a lack of commercially available analogues and/or suitable synthetic methodology. This represents an opportunity for the development of new synthetic research to enable rapid access to novel chemical space and fragment optimisation.

Positional Analogue Scanning: An Effective Strategy for Multiparameter Optimization in Drug Design

Minimizing the number and duration of design cycles needed to optimize hit or lead compounds into high-quality chemical probes or drug candidates is an ongoing challenge in biomedical research. Small structure modifications to hit or lead compounds can have meaningful impacts on pharmacological profiles due to significant effects on molecular and physicochemical properties and intra- and intermolecular interactions. Rapid pharmacological profiling of an efficiently prepared series of positional analogues stemming from the systematic exchange of methine groups with heteroatoms or other substituents in aromatic or heteroaromatic ring-containing hit or lead compounds is one approach toward minimizing design cycles (e.g., exchange of aromatic or heteroaromatic CH groups with N atoms or CF, CMe, or COH groups). In this Perspective, positional analogue scanning is shown to be an effective strategy for multiparameter optimization in drug design, whereby substantial improvements in a variety of pharmacological parameters can be achieved.

Oxidative Cyclization Approach to Benzimidazole Libraries

An efficient approach to the parallel synthesis of benzimidazoles from anilines is described. Library approaches to vary the N1 and C2 vectors of benzimidazoles are well established; however, C4-C7 variation has traditionally relied on 1,2-dianiline building blocks, providing limited chemical space coverage. We have developed an amidine formation/oxidative cyclization sequence that enables anilines as a diversity set for benzimidazole C4-C7 SAR generation in parallel format. The amidine annulation was achieved using PIDA or Cu-mediated oxidation to access both N-H and N-alkyl benzimidazoles. This library protocol has now been utilized for analog production in four medicinal chemistry projects. Additionally, the synthesis of aza-benzimidazoles from aminopyridines was achieved via an analogous sequence.