Implementation of an AI-assisted fragment-generator in an open-source platform.

We recently reported a deep learning model to facilitate fragment library design, which is critical for efficient hit identification. However, our model was implemented in Python. We have now created an implementation in the KNIME graphical pipelining environment which we hope will allow experimentation by users with limited programming knowledge.

Fragment-based drug discovery-the importance of high-quality molecule libraries.

Fragment-based drug discovery (FBDD) is now established as a complementary approach to high-throughput screening (HTS). Contrary to HTS, where large libraries of drug-like molecules are screened, FBDD screens involve smaller and less complex molecules which, despite a low affinity to protein targets, display more 'atom-efficient' binding interactions than larger molecules. Fragment hits can, therefore, serve as a more efficient start point for subsequent optimisation, particularly for hard-to-drug targets.

Stabilization of the RAS:PDE6D Complex Is a Novel Strategy to Inhibit RAS Signaling.

RAS is a major anticancer drug target which requires membrane localization to activate downstream signal transduction. The direct inhibition of RAS has proven to be challenging. Here, we present a novel strategy for targeting RAS by stabilizing its interaction with the prenyl-binding protein PDE6D and disrupting its localization.

Automated Generation of Novel Fragments Using Screening Data, a Dual SMILES Autoencoder, Transfer Learning and Syntax Correction.

Fragment-based hit identification (FBHI) allows proportionately greater coverage of chemical space using fewer molecules than traditional high-throughput screening approaches. However, effectively exploiting this advantage is highly dependent on the library design. Solubility, stability, chemical complexity, chemical/shape diversity, and synthetic tractability for fragment elaboration are all critical aspects, and molecule design remains a time-consuming task for computational and medicinal chemists.

Re-introducing non-optimal synonymous codons into codon-optimized constructs enhances soluble recovery of recombinant proteins from Escherichia coli.

Gene synthesis services have largely superseded traditional PCR methods for the generation of cDNAs destined for bacterial expression vectors. This, in turn, has increased the application of codon-optimized cDNAs where codons rarely used by Escherchia coli are replaced with common synonymous codons to accelerate translation of the target. A markedly accelerated rate of expression often results in a significant uplift in the levels of target protein but a substantial proportion of the enhanced yield can partition to the insoluble fraction rendering a significant portion of the gains unavailable for native purification.

Structure-based design, synthesis and biological evaluation of a novel series of isoquinolone and pyrazolo[4,3-c]pyridine inhibitors of fascin 1 as potential anti-metastatic agents.

Fascin is an actin binding and bundling protein that is not expressed in normal epithelial tissues but overexpressed in a variety of invasive epithelial tumors. It has a critical role in cancer cell metastasis by promoting cell migration and invasion. Here we report the crystal structures of fascin in complex with a series of novel and potent inhibitors.

A Novel Small-Molecule Inhibitor of MRCK Prevents Radiation-Driven Invasion in Glioblastoma.

Glioblastoma (GBM) is an aggressive and incurable primary brain tumor that causes severe neurologic, cognitive, and psychologic symptoms. Symptoms are caused and exacerbated by the infiltrative properties of GBM cells, which enable them to pervade the healthy brain and disrupt normal function. Recent research has indicated that although radiotherapy (RT) remains the most effective component of multimodality therapy for patients with GBM, it can provoke a more infiltrative phenotype in GBM cells that survive treatment.

Discovery of Potent and Selective MRCK Inhibitors with Therapeutic Effect on Skin Cancer.

The myotonic dystrophy-related Cdc42-binding kinases MRCKα and MRCKβ contribute to the regulation of actin-myosin cytoskeleton organization and dynamics, acting in concert with the Rho-associated coiled-coil kinases ROCK1 and ROCK2. The absence of highly potent and selective MRCK inhibitors has resulted in relatively little knowledge of the potential roles of these kinases in cancer. Here, we report the discovery of the azaindole compounds BDP8900 and BDP9066 as potent and selective MRCK inhibitors that reduce substrate phosphorylation, leading to morphologic changes in cancer cells along with inhibition of their motility and invasive character.

A fully automated procedure for the parallel, multidimensional purification and nucleotide loading of the human GTPases KRas, Rac1 and RalB.

Small GTPases regulate many key cellular processes and their role in human disease validates many proteins in this class as desirable targets for therapeutic intervention. Reliable recombinant production of GTPases, often in the active GTP loaded state, is a prerequisite for the prosecution of drug discovery efforts. The preparation of these active forms can be complex and often constricts the supply to the reagent intensive techniques used in structure base drug discovery.

Identification of a Selective G1-Phase Benzimidazolone Inhibitor by a Senescence-Targeted Virtual Screen Using Artificial Neural Networks.

Cellular senescence is a barrier to tumorigenesis in normal cells, and tumor cells undergo senescence responses to genotoxic stimuli, which is a potential target phenotype for cancer therapy. However, in this setting, mixed-mode responses are common with apoptosis the dominant effect. Hence, more selective senescence inducers are required.

A novel small-molecule MRCK inhibitor blocks cancer cell invasion.

Background: The myotonic dystrophy kinase-related CDC42-binding kinases MRCKα and MRCKβ regulate actin-myosin contractility and have been implicated in cancer metastasis. Along with the related ROCK1 and ROCK2 kinases, the MRCK proteins initiate signalling events that lead to contractile force generation which powers cancer cell motility and invasion. A potential strategy for cancer therapy is to reduce metastasis by blocking MRCK activity, either alone or in combination with ROCK inhibition.

The first intramolecular silene Diels-Alder reactions.

The synthesis of silaheterocycles through the first examples of an intramolecular silene Diels-Alder reaction is described.

Fragment-based hit identification: thinking in 3D.

The identification of high-quality hits during the early phases of drug discovery is essential if projects are to have a realistic chance of progressing into clinical development and delivering marketed drugs. As the pharmaceutical industry goes through unprecedented change, there are increasing opportunities to collaborate via pre-competitive networks to marshal multifunctional resources and knowledge to drive impactful, innovative science. The 3D Fragment Consortium is developing fragment-screening libraries with enhanced 3D characteristics and evaluating their effect on the quality of fragment-based hit identification (FBHI) projects.

Using fragment-based technologies to target protein-protein interactions.

Whilst fragment-based screening has found significant utility in aiding the discovery of high quality hits against a range of targets, the use of this technology in the protein-protein interaction inhibitor field is very much in its infancy. This review aims to highlight the key technologies used to identify fragment hits, such as NMR, SPR, X-ray crystallography and biochemical screening, the fragment-based protein-protein interaction case studies reported to date and, more importantly, the potential of this methodology in unearthing high quality hit molecules in this critical area of drug discovery. In addition, we also discuss some of the key aspects of fragment library design, the composition of a high quality library and suggest ways in which future, more structurally diverse fragments which occupy different regions of chemical space to the vast majority of current fragment libraries may be selected.

The design and synthesis of novel, potent and orally bioavailable N-aryl piperazine-1-carboxamide CCR2 antagonists with very high hERG selectivity.

A novel N-aryl piperazine-1-carboxamide series of human CCR2 chemokine receptor antagonists was discovered. Early analogues were potent at CCR2 but also inhibited the hERG cardiac ion channel. Structural modifications which decreased lipophilicity and basicity resulted in the identification of a sub-series with an improved margin over hERG.

Acyl polysilanes: new acyl anion equivalents for additions to electron-deficient alkenes.

Silenes, generated through thermolysis of acylpolysilanes, add to alpha,beta-unsaturated esters to form cyclobutanes and silylsubstituted cyclopropanes in moderate yields. Upon Si-C bond oxidation the cyclopropanes are converted directly to 1,4-dicarbonyl compounds, thus demonstrating the formal acyl anion chemistry of acyl polysilanes.

One-pot multistep Bohlmann-Rahtz heteroannulation reactions: synthesis of dimethyl sulfomycinamate.

[reaction: see text] The synthesis of dimethyl sulfomycinamate, the acidic methanolysis product of the sulfomycin family of thiopeptide antibiotics, from methyl 2-oxo-4-(trimethylsilyl)but-3-ynoate is achieved in a 2,3,6-trisubstituted pyridine synthesis that proceeds with total regiocontrol in 13 steps by the Bohlmann-Rahtz heteroannulation of a 1-(oxazol-4-yl)enamine or in 12 steps and 9% yield by three-component cyclocondensation with N-[3-oxo-3-(oxazol-4-yl)propanoyl]serine and ammonia in ethanol.

Structure-guided design of pyrazolo[1,5-a]pyrimidines as inhibitors of human cyclin-dependent kinase 2.

The protein structure guided design of a series of pyrazolo[1,5-a]pyrimidines with high potency for human cyclin-dependent kinase 2 (CDK2) is described. Some examples were shown to inhibit the growth of human colon tumour cells, were equipotent for CDK1 and were selective against GSK-3beta and other kinases.

Structure-based drug design targeting an inactive RNA conformation: exploiting the flexibility of HIV-1 TAR RNA.

The targeting of RNA for the design of novel anti-viral compounds represents an area of vast potential. We have used NMR and computational methods to model the interaction of a series of synthetic inhibitors of the in vitro RNA binding activities of a peptide derived from the transcriptional activator protein, Tat, from human immunodeficiency virus type 1. Inhibition has been measured through the monitering of fluorescence resonance energy transfer between fluorescently labeled peptide and RNA components.

Rational design of inhibitors of HIV-1 TAR RNA through the stabilisation of electrostatic "hot spots".

The targeting of RNA for the design of novel anti-viral compounds has until now proceeded largely without incorporating direct input from structure-based design methodology, partly because of lack of structural data, and complications arising from substrate flexibility. We propose a paradigm to explain the physical mechanism for ligand-induced refolding of trans-activation response element (TAR RNA) from human immunodeficiency virus 1 (HIV-1). Based upon Poisson-Boltzmann analysis of the TAR structure, as bound by a peptide derived from the transcriptional activator protein, Tat, our hypothesis shows that two specific electrostatic interactions are necessary to stabilise the conformation.

First synthesis of an amythiamicin pyridine cluster.

The pyridine-containing central domain of the amythiamicin group of thiopeptide antibiotics is prepared in protected form in 9 steps, 93%ee and 18% overall yield from (S)-2-[1-(tert-butoxycarbonylamino)-2-methylpropyl]thiazole-4-carboxylic acid by Michael addition-cyclodehydration of a 2-(2-thiazolyl)enamine and 1-(2-thiazolyl)propynone.

Synthesis of dimethyl sulfomycinamate.

[reaction: see text] Dimethyl sulfomycinamate, the oxazole-thiazole-pyridine product generated in the methanolysis of the thiopeptide antibiotic sulfomycin I, is prepared in 13 steps and 8% overall yield by the Bohlmann-Rahtz heteroannulation of 1-(oxazol-4-yl)enamines and methyl 4-(trimethylsilyl)-2-oxobut-3-ynoate.

Structure-based design of agents targeting the bacterial ribosome.

Rational structure-based drug design has been applied to the antibiotic thiostrepton, in an attempt to overcome some of its' limitations. The identification of a proposed binding fragment allowed construction of a number of key fragments, which were derivatised to generate a library of potential antibiotics. These were then evaluated to determine their ability to bind to the L11 binding domain of the prokaryotic ribosome and inhibit bacterial protein translation.

A facile solution phase combinatorial synthesis of tetrasubstituted pyridines using the Bohlmann-Rahtz heteroannulation reaction.

The solution phase combinatorial Bohlmann-Rahtz reaction gives highly functionalized pyridine libraries from enamino esters and alkynones in a single synthetic step. Good product ratios and library purities were obtained in reactions catalyzed by zinc(II) bromide, the acid-catalyzed heteroannulation procedure offering considerable improvements over traditional methodology.

A new one-pot three-component condensation reaction for the synthesis of 2,3,4,6-tetrasubstituted pyridines.

The one-pot three-component condensation of a beta-ketoester, ammonia and an alkynone in the presence of a Brønsted or Lewis acid or Amberlyst 15 ion exchange resin provided 2,3,6-trisubstituted or 2,3,4,6-tetrasubstituted pyridines directly in good yield and with total regiocontrol.