Recent developments in combinatorial organic synthesis

Stereodivergent Rhodium(III)-Catalyzed cis-Cyclopropanation Enabled by Multivariate Optimization

The design of stereodivergent transformations is of great interest to the synthetic community as it allows funneling of a given reaction pathway toward one stereochemical outcome or another by only minor adjustments of the reaction setup. Herein, we present a physical organic approach to invert the sense of induction in diastereoselective cyclopropanation of alkenes with N-enoxyphthalimides through rhodium(III) catalysis. Careful parametrization of catalyst-substrate molecular determinants allowed us to interrogate linear-free energy relationships and establish an intuitive and robust statistical model that correlates an extensive number of data points in high accuracy. Our multivariate correlations-steered mechanistic investigation culminated with a robust and general diastereodivergent cyclopropanation tool where the switch from trans- to cis-diastereoinduction is attributed to a mechanistic dichotomy. Selectivity might be determined by the flexibility of rhodacyclic intermediates derived from ring-opened versus -unopened phthalimides, induced by both their respective ring size and the Sterimol B1 parameter of the CpX ligand on rhodium.

Adversarial Threshold Neural Computer for Molecular de Novo Design

In this article, we propose the deep neural network Adversarial Threshold Neural Computer (ATNC). The ATNC model is intended for the de novo design of novel small-molecule organic structures. The model is based on generative adversarial network architecture and reinforcement learning. ATNC uses a Differentiable Neural Computer as a generator and has a new specific block, called adversarial threshold (AT). AT acts as a filter between the agent (generator) and the environment (discriminator + objective reward functions). Furthermore, to generate more diverse molecules we introduce a new objective reward function named Internal Diversity Clustering (IDC). In this work, ATNC is tested and compared with the ORGANIC model. Both models were trained on the SMILES string representation of the molecules, using four objective functions (internal similarity, Muegge druglikeness filter, presence or absence of sp³-rich fragments, and IDC). The SMILES representations of 15K druglike molecules from the ChemDiv collection were used as a training data set. For the different functions, ATNC outperforms ORGANIC. Combined with the IDC, ATNC generates 72% of valid and 77% of unique SMILES strings, while ORGANIC generates only 7% of valid and 86% of unique SMILES strings. For each set of molecules generated by ATNC and ORGANIC, we analyzed distributions of four molecular descriptors (number of atoms, molecular weight, logP, and tpsa) and calculated five chemical statistical features (internal diversity, number of unique heterocycles, number of clusters, number of singletons, and number of compounds that have not been passed through medicinal chemistry filters). Analysis of key molecular descriptors and chemical statistical features demonstrated that the molecules generated by ATNC elicited better druglikeness properties. We also performed in vitro validation of the molecules generated by ATNC; results indicated that ATNC is an effective method for producing hit compounds.

Divergent solid-phase synthesis of natural product-inspired bipartite cyclodepsipeptides: total synthesis of seragamide A

Macrocyclic natural products (NPs) and analogues thereof often show high affinity, selectivity, and metabolic stability, and methods for the synthesis of NP-like macrocycle collections are of major current interest. We report an efficient solid-phase/cyclorelease method for the synthesis of a collection of macrocyclic depsipeptides with bipartite peptide/polyketide structure inspired by the very potent F-actin stabilizing depsipeptides of the jasplakinolide/geodiamolide class. The method includes the assembly of an acyclic precursor chain on a polymeric carrier, terminated by olefins that constitute complementary fragments of the polyketide section and cyclization by means of a relay-ring-closing metathesis (RRCM). The method was validated in the first total synthesis of the actin-stabilizing cyclodepsipeptide seragamide A and the synthesis of a collection of structurally diverse bipartite depsipeptides.

An automated, polymer-assisted strategy for the preparation of urea and thiourea derivatives of 15-membered azalides as potential antimalarial chemotherapeutics

A series of 15-membered azalide urea and thiourea derivatives has been synthesized and evaluated for their in vitro antimalarial activity against chloroquine-sensitive (D6), chloroquine/pyremethamine resistant (W2) and multidrug resistant (TM91C235) strains of Plasmodium falciparum. We have developed an effective automated synthetic strategy for the rapid synthesis of urea/thiourea libraries of a macrolide scaffold. Compounds have been synthesized using a solution phase strategy with overall yields of 50-80%. Most of the synthesized compounds had inhibitory effects. The top 10 compounds were 30-65 times more potent than azithromycin, an azalide with antimalarial activity, against all three strains.

Fully automated flow-through synthesis of secondary sulfonamides in a binary reactor system

A fully automated flow-through process for the production of secondary sulfonamides is presented. Primary sulfonamides were monoalkylated using a two-step "catch and release" protocol to generate library products of high purity. The automated flow synthesis platform incorporates four independent reactor columns and is able to perform automated column regeneration. A 48-member sulfonamide library was prepared as two 24-member sublibraries, affording library compounds in good yields and high purities without the need for further column chromatographic purification.

Application of the solid-phase Julia-Lythgoe olefination in vitamin D side-chain construction

An example of the Julia-Lythgoe attachment of the vitamin D side chain to a solid-phase linked Inhoffen-Lythgoe diol derived CD-ring fragment is reported.

Solid-phase synthesis of 1,3,4-oxadiazoline-5-thione derivatives from resin-bound acylhydrazines

A new strategy for solid-phase synthesis of 2,5-disubstituted 1,3,4-oxadiazoles has been developed. The 1,3,4-oxadiazoline-5-thione derivatives were synthesized from resin-bound acylhydrazines in several steps providing 78-88% overall yields and excellent purity.

Evaluation of Solution and Solid-Phase Approaches to the Synthesis of Libraries of α,α-Disubstituted-α-acylaminoketones

Solid phase, solution, and hybrid approaches to the synthesis of small focused libraries of alpha,alpha-disubstituted-alpha-acylaminoketones have been explored. Solution and hybrid approaches that used support-bound reagents and scavenger resins were the most productive.

Solid-Phase Synthesis of 2-Aminoquinazolinone Derivatives with Two- and Three-Point Diversity

A versatile solid-phase method for the synthesis of various substituted 2-amino-4(3H)-quinazolinones with two- and three-point diversity is described. The synthesis commenced with the generation of polymer-bound S-methylisothiourea followed by N-acylation with different substituted o-nitrobenzoic acid. Finally, reduction of the nitro group triggered intramolecular cyclization via formation of guanidine to afford 2-amino-4(3H)-quinazolinone and its derivatives in high yields and purities.

Automated flow-through synthesis of heterocyclic thioethers

The fully automated, sequential flow-through synthesis of a 44-member array of thioethers 10[1-4,1-11] employing a resin "capture and release" reactor column is described. The array incorporates four different heterocyclic scaffolds, and the synthesis was performed using a custom-built robotic synthesizer that is able to (i) load and regenerate the reactor column and (ii) array each product into a single vial using UV threshold detection. All the compounds were obtained in high yield (>75%) and excellent purity (>95%) without the need for further purification.

A Highly Automated, Polymer-Assisted Strategy for the Preparation of 2-Alkylthiobenzimidazoles andN,N‘-Dialkylbenzimidazolin-2-ones

A multistep, polymer-assisted solution phase strategy for the highly automated (auto-PASP) synthesis of 2-alkylthiobenzimidazole and N,N'-dialkylbenzimidazolin-2-one libraries is presented. The approach incorporates in-line purification techniques to afford library products directly with high purities and is exemplified by the preparation of a 96-member 2-alkylthiobenzimidazoline library 1[1-12,1-8] and a 72-member N,N'-dialkylbenzimidazolin-2-one library 9[1-12,1-6].

Solid-phase intramolecular N-acyliminium Pictet-Spengler reactions as crossroads to scaffold diversity

A novel solid-phase intramolecular Pictet-Spengler reaction is presented. The approach utilizes masked aldehyde building blocks protected as their N-Boc-1,3-oxazinanes for the clean generation of solid-supported aldehydes. When exposed to simple acidic treatment, the aldehyde functionality is rapidly released and becomes susceptible to nucleophilic attack from an amide nitrogen of the peptide backbone, which results in the formation of a highly reactive cyclic N-acyliminium ion. Subsequently, a quantitative and highly stereoselective Pictet-Spengler reaction takes place by attack of the indole from a neighboring tryptophan, thus appending two new N-fused rings to the indole moiety. Extension of this intramolecular reaction to substituted indoles, and other reactive heterocycles, such as furane and thiophenes, provides a convenient and rapid access to a range of pharmacologically interesting tri- and tetracyclic scaffolds. Finally, the reaction products may conveniently be released from the solid support (PEGA) by cleavage of the base-labile linker (HMBA).

Fully Automated Polymer-Assisted Synthesis of 1,5-Biaryl Pyrazoles

The polymer-assisted solution-phase (PASP) synthesis of a 192-member 2-D array of 1,5-biaryl pyrazoles 4[1-12,1-16] is reported. The synthesis was performed in a fully automated manner using a multiprobe top-filtration robot and incorporates a "catch and release" step to afford library compounds directly in high yield and purity.