Rapid Hit Research Articles

Rapid PROTAC Discovery Platform: Nanomole-Scale Array Synthesis and Direct Screening of Reaction Mixtures.

Precise length, shape, and linker attachment points are all integral components to designing efficacious proteolysis targeting chimeras (PROTACs). Due to the synthetic complexity of these heterobifunctional degraders and the difficulty of computational modeling to aid PROTAC design, the exploration of structure-activity relationships remains mostly empirical, which requires a significant investment of time and resources. To facilitate rapid hit finding, we developed capabilities for PROTAC parallel synthesis and purification by harnessing an array of preformed E3-ligand-linker intermediates. In the next iteration of this approach, we developed a rapid, nanomole-scale PROTAC synthesis methodology using amide coupling that enables direct screening of nonpurified reaction mixtures in cell-based degradation assays, as well as logD and EPSA measurements. This approach greatly expands and accelerates PROTAC SAR exploration (5 days instead of several weeks) as well as avoids laborious and solvent-demanding purification of the reaction mixtures, thus making it an economical and more sustainable methodology for PROTAC hit finding.

Analysis of rapid HIT application to touch DNA samples.

Rapid DNA technology is being utilized for reference profiles worldwide. There is also strong data in the literature to support its use for high-template DNA sources, the same is not true for low-template sources, such as touch DNA; this is a requirement before wider implementation to forensic casework is considered. We report on the Rapid HIT Intel cartridge's ability to facilitate successful amplification of touch DNA to obtain profiles from template deposited on items commonly encountered in forensic casework. Eight items were touched in ten replicates- two were tapelifted, three swabbed, and three directly inserted. Significance was observed in the alleles amplified and RFU with respect to sample type. Three samples performed well: cable tie, fabric, and matchstick. As two of these were directly inserted, this should be considered for any sample small enough. Placement of highly absorbent substrates into the cartridge is not advised as it can cause a lysate-pull error. Heterozygote loci often presented as homozygous (32%-78% loci per profile); this was influenced by substrate type and profile RFU. Loci with larger masses exhibited higher false homozygosity also. Comparison of the donor's profile analyzed was performed against previous datasets analyzing touch DNA through standard workflow, including manual DNA extraction, PCR, and CE separation. These data show that for all substrates, except for a fabric swatch, standard processing is preferential to Rapid HIT analysis. In its current form, rapid DNA technology is not fit for the routine analysis of touch DNA samples in forensic casework.

Synthesis of Arylethylamines via C(sp3)-C(sp3) Palladium-Catalyzed Cross-Coupling.

Substituted arylethylamines represent a key structural motif in natural, pharmaceutical, and agrochemical compounds. Access to such scaffolds has been the subject of long-standing synthetic interest. Herein, we report the synthesis of such scaffolds via a palladium-catalyzed C(sp3)-C(sp3) coupling between (chloromethyl)aryls and air-/moisture-stable N,N-dialkylaminomethyltrifluoroborate salts. Rapid hit identification was achieved using microscale high-throughput experimentation and was followed by millimolar-scale reaction parameter optimization. A range of structurally and electronically varied arylethylamine products were obtained in moderate to excellent yields (27-96%, >60 examples). The reaction mechanism is proposed to proceed via formation of a trialkylbenzylammonium species prior to oxidative addition.

Collaborative virtual screening to elaborate an imidazo[1,2-a]pyridine hit series for visceral leishmaniasis.

An innovative pre-competitive virtual screening collaboration was engaged to validate and subsequently explore an imidazo[1,2-a]pyridine screening hit for visceral leishmaniasis. In silico probing of five proprietary pharmaceutical company libraries enabled rapid expansion of the hit chemotype, alleviating initial concerns about the core chemical structure while simultaneously improving antiparasitic activity and selectivity index relative to the background cell line. Subsequent hit optimization informed by the structure–activity relationship enabled by this virtual screening allowed thorough investigation of the pharmacophore, opening avenues for further improvement and optimization of the chemical series.

CcpNmr AnalysisScreen, a new software programme with dedicated automated analysis tools for fragment-based drug discovery by NMR

Fragment-based drug discovery or FBDD is one of the main methods used by industry and academia for identifying drug-like candidates in early stages of drug discovery. NMR has a significant impact at any stage of the drug discovery process, from primary identification of small molecules to the elucidation of binding modes for guiding optimisations. The essence of NMR as an analytical tool, however, requires the processing and analysis of relatively large amounts of single data items, e.g. spectra, which can be daunting when managed manually. One bottleneck in FBDD by NMR is a lack of adequate and well-integrated resources for NMR data analysis that are freely available to the community. Thus, scientists typically resort to manually inspecting large datasets and relying predominantly on subjective interpretations. In this manuscript, we present CcpNmr AnalysisScreen, a software package that provides computational tools for automated analysis of FBDD data by NMR. We outline how the quality of collected spectra can be evaluated quickly, and how robust workflows can be optimised for reliable and rapid hit identification. With an intuitive graphical user interface and powerful algorithms, AnalysisScreen enables easy analysis of the large datasets needed in the early process of drug discovery by NMR.

Demonstration of the utility of DOS-derived fragment libraries for rapid hit derivatisation in a multidirectional fashion.

Organic synthesis underpins the evolution of weak fragment hits into potent lead compounds. Deficiencies within current screening collections often result in the requirement of significant synthetic investment to enable multidirectional fragment growth, limiting the efficiency of the hit evolution process. Diversity-oriented synthesis (DOS)-derived fragment libraries are constructed in an efficient and modular fashion and thus are well-suited to address this challenge. To demonstrate the effective nature of such libraries within fragment-based drug discovery, we herein describe the screening of a 40-member DOS library against three functionally distinct biological targets using X-Ray crystallography. Firstly, we demonstrate the importance for diversity in aiding hit identification with four fragment binders resulting from these efforts. Moreover, we also exemplify the ability to readily access a library of analogues from cheap commercially available materials, which ultimately enabled the exploration of a minimum of four synthetic vectors from each molecule. In total, 10–14 analogues of each hit were rapidly accessed in three to six synthetic steps. Thus, we showcase how DOS-derived fragment libraries enable efficient hit derivatisation and can be utilised to remove the synthetic limitations encountered in early stage fragment-based drug discovery.

Monash Fragment Platform

The Monash Fragment Platform (MFP) provides academic and commercial researchers with access to fragment-based drug discovery (FBDD) technologies for their therapeutic targets. The facilities are located at the Monash Institute for Pharmaceutical Sciences (MIPS) in Parkville, Australia's largest and most successful pharmaceutical institute. FBDD screening uses our high-quality, in-house fragment library designed to maximise chemical space coverage and enable rapid hit optimisation. Screening cascades are tailored for each target and can be performed using a variety of techniques including NMR spectroscopy and our state-of-the-art surface plasmon resonance (SPR) facility. Structural biology and medicinal chemistry expertise utilising our standardized REFIL strategy enables the rapid elaboration of fragments into leads without the requirement for a large chemistry program.

Targeting the Transcriptional Addiction of Leukemia Stem Cells By a New Class of Protein Kinase Inhibitors

Cancer stem cells present a major therapeutic challenge - their effective eradication depends on therapeutic targeting of the relative vulnerabilities of the cancer stem cells vs. normal tissue stem cells. One feature that distinguishes cancer initiating and propagating cells from their normal counterparts is transcriptional addiction, providing opportunities for novel therapeutic interventions with the aim of curing cancer.CKIα ablation appears as a promising means of activating p53 and killing leukemia cells in MDS and AML (Elyada et al , doi:10.1038/nature09673; Kronke et al, doi: 10.1038/nature14610); yet, with no selective CKIα inhibitors for in vivo use, the therapeutic value of CKIα inhibition cannot be validated. We succeeded in developing two different classes of CKIα inhibitors, one inducing CKIα degradation, and another targeting the catalytic pocket of CKIα, with no degradation. Both inhibitor types activate p53, yet we found that CKIα ablation or degradation was not sufficient to selectively eliminate leukemia stem cells, due to robust expression of anti-apoptotic oncogenes driven by super-enhancer activation.Through extensive medicinal chemistry, we obtained CKIα catalytic inhibitors with profound killing capacity of primary mouse AML cells and human AML cell lines. We demonstrated a strong therapeutic effect in a mouse model of MLL-AF9-induced leukemia, with >40% cure rates evident by transplantation of bone marrow from treated leukemic mice to lethally irradiated normal mice. All transplanted mice regained normal blood counts, exclusively derived from the donor bone marrow. None showed any evidence of residual disease for 6 months, demonstrating a successful therapeutic window, distinguishing leukemia stem cells (LSCs) from HSPCs. Parallel in vitro experiments, show that the inhibitors did not affect normal hematopoietic progenitors in a CFU assay, but eliminated AML progenitors at an IC50 <9nM.We found that CKIα inhibitors possessing potent anti-leukemia activity are distinguished by their capacity to co-target CDK9 and suppress the RNA Pol II elongation factor P-TEFb (CDK9-CyclinT1 complex), evident by blocking the phosphorylation of RNA Pol II C-terminal domain (pCTD2/5, see Figure). Co-crystallography studies elucidated the structural basis for co-targeting of CKIα and P-TEFb, the latter controls the rate limiting step of Poll-II-transcription and functions as a gatekeeper of super-enhancers. We found that both P-TEFb and super-enhancer activity are vigorously activated in AML cells. Therefore, the efficient P-TEFb-targeting activity of the inhibitors enables a selective blockade of leukemia super-enhancers (SE)-driven transcription, demonstrated by ChIP-seq analysis. As a result, SE-dependent transcription of major leukemia drivers including Myc and the anti-apoptotic oncogenes Bcl-2 and Mcl-1 was nearly abolished.Another remarkable feature of these dual CKIα-P-TEFb inhibitors is a rapid hit mechanism, by which, short drug exposure (10 mins in vitro and 2hrs in vivo) results in prolonged (24hrs) SE suppression and leukemia cell apoptosis. This unique property, which is at variance with the current occupancy-driven pharmacological paradigm, likely contributes to the dramatic therapeutic effect of co-targeting CKIα and P-TEFb in leukemia, whereby combination of rapid p53 induction with disruption of oncogenic super-enhancers eliminates leukemia stem cells without compromising normal HSPCs. The ability to disrupt super-enhancers and eliminate their associated oncogenes within minutes of drug exposure permits short intermittent therapy, which minimizes generalized toxicity. Indeed, at the therapeutic dose, we did not observe any significant adverse treatment effects even at daily treatment for 45 days in mice.To conclude, we developed a new class of small molecule inhibitors that co-targets CKIα and P-TEFb. These inhibitors have unique pharmacologic properties: short-term kinase inhibition results in long-term disruption of SE activity. Shutdown of leukemic super-enhancers in synergy with robust p53 activation compromises leukemic cells and stem cells addicted to SE-driven transcription. These features explain the powerful and specific anti-leukemic therapeutic effects of this new class of inhibitors in-vivo. [Display omitted] DisclosuresBen-Neriah:BioTheryX Inc.: Consultancy, Equity Ownership, Research Funding. Vacca:BioTheryX Inc.: Consultancy. Mercurio:BioTheryX: Employment, Equity Ownership.

Implementation of a rapid HIT immunoassay at a university hospital – Retrospective analysis of HIT laboratory orders in patients with thrombocytopenia

BackgroundHeparin-induced thrombocytopenia (HIT) is a rare cause of thrombocytopenia and a potentially life-threatening adverse drug reaction. Clinical overdiagnosis of HIT results in costly laboratory tests and anticoagulation. Criteria and algorithms for diagnosis are established, but their translation into clinical practice is still challenging. Study design and methodsIn a retrospective approach we studied all HIT related laboratory test requests within four years and evaluated data before (1st period, 24month) and after (2nd period, 24month) replacing particle gel immunoassay (PaGIA) and enzyme-linked immunosorbent assay (ELISA) by a chemiluminescent immunoassay (CLIA). HIT was confirmed by heparin-induced platelet activation (HIPA) test. Clinical pretest probability for HIT using an implemented simplified 4Ts score and platelet count were evaluated. Costs for laboratory tests and alternative anticoagulation were calculated. ResultsIn 1850 patients with suspected HIT, 2327 laboratory orders were performed. In 87.2% of these orders an intermediate/high simplified 4Ts score was found. Thrombocytopenia was present in 87.1%. After replacing PaGIA and ELISA by CLIA the number of immunological and functional laboratory tests was reduced by 38.2%. The number of positive HIT immunoassays declined from 22.6% to 6.0%, while the number of positive HIPA tests among positive immunological tests increased by 19%. Altogether, acute HIT was confirmed in 59 patients. A decline in the use of alternative anticoagulants was observed in the 2nd period. ConclusionOur study shows that in a university hospital setting HIT is well-known, but diagnosis requires a precise laboratory confirmation. Replacing PaGIA and ELISA by CLIA did not influence laboratory order behavior but results in reduced overall costs for laboratory diagnostics and alternative anticoagulation.

Application of Off-Rate Screening in the Identification of Novel Pan-Isoform Inhibitors of Pyruvate Dehydrogenase Kinase.

Libraries of nonpurified resorcinol amide derivatives were screened by surface plasmon resonance (SPR) to determine the binding dissociation constant (off-rate, kd) for compounds binding to the pyruvate dehydrogenase kinase (PDHK) enzyme. Parallel off-rate measurements against HSP90 and application of structure-based drug design enabled rapid hit to lead progression in a program to identify pan-isoform ATP-competitive inhibitors of PDHK. Lead optimization identified selective sub-100-nM inhibitors of the enzyme which significantly reduced phosphorylation of the E1α subunit in the PC3 cancer cell line in vitro.

A natural substrate-based fluorescence assay for inhibitor screening on diacylglycerol lipase α

The endocannabinoid 2-arachidonoylglycerol (2-AG) is predominantly biosynthesized by sn-1-diacylglycerol lipase α (DAGL-α) in the CNS. Selective inhibitors of DAGL-α will provide valuable insights in the role of 2-AG in endocannabinoid signaling processes and are potential therapeutics for the treatment of obesity and neurodegenerative diseases. Here, we describe the development of a natural substrate-based fluorescence assay for DAGL-α, using a coupled enzyme approach. The continuous setup of our assay allows monitoring of DAGL-α activity in real-time and in a 96-well plate format. This constitutes a major improvement to the currently available radiometric and LC/MS-based methods, which can be executed only in low-throughput formats. In addition, our assay circumvents the use of radioactive material. We demonstrate that our assay can be used to screen inhibitors of DAGL-α activity, using 1-stearoyl-2-arachidonoyl-sn-glycerol as the physiologically relevant natural substrate of DAGL-α. Furthermore, our method can be employed to measure DAGL activity and inhibition in the mouse brain membrane proteome. Consequently, our assay should serve as a valuable tool for rapid hit validation and lead optimization of DAGL-α inhibitors.

107 Genomes to hit molecules In Silico: a country path today, a highway tomorrow: a case study of Chikungunya

The growing genomic and proteomic sequence/structural databases trigger high expectations for a rapid and successful treatment of diseases and disorders. In the current biological information, rich and functional knowledge, poor scenario, the feasibility of creating an automated genomes to hits (G2H) assembly line in order to cut down the cost and time in drug discovery is discussed. The G2H computational pathway involves several challenging research areas viz. functional annotation of genomes, identification of druggable targets, prediction of three-dimensional structures of protein targets from their amino acid sequences, and hit molecule generation for these targets followed by a transition from bench to bedside. We describe the ‘G2H In Silico’ strategy (called Dhanvantari), and illustrate it on Chikungunya virus (CHIKV). G2H is a novel pathway incorporating, a series of steps such as gene prediction (Chemgenome), protein tertiary structure determination (Bhageerath), automated active site identification, rapid hit molecule generation followed by atomic level docking and scoring of hits to arrive at lead compounds (Sanjeevini). The current state of the art for each of the steps in the pathway will be highlighted and the results will be presented and discussed.

Online parallel fragment screening and rapid hit exploration for nicotinic acetylcholine receptors

An online bioaffinity analysis system was used to screen our in-house fragment library on two related proteins, Ls- and Ac-AChBP, model proteins for nAChRs, in particular the α7 subtype. An efficient protocol for medium throughput fragment screening, hit validation and affinity ranking after single concentration injections was developed. The screening of the fragment library and the good correlation between online estimated pKi values (derived from a single injection) and pKi values measured with a radioligand binding assay (RBA, full range concentration curve) have proven the value of the online fluorescence enhancement assay in FBDD. The online bioaffinity system was also used for rapid hit exploration using single point injections of combinatorial libraries at 96-well format. This led to the discovery of an optimized hit with micromolar affinity towards the α7 nAChR.

A New Rapid Test for the Detection of PF4:Heparin Antibodies.

AbstractAbstract 3708Heparin Induced Thrombocytopenia (HIT), the most frequent drug-induced immune-mediated type of thrombocytopenia, is an important and sometimes life-threatening complication of heparin therapy. HIT can be triggered by standard therapeutic dose heparin, low-dose (prophylactic treatment), low molecular weight heparin, unfractionated heparin and even by minute quantities given to flush intravascular catheters.HIT is a clinicopathologic syndrome cause by platelet activating antibodies that recognize complexes of platelet factor 4 and heparin (PF4-heparin). Thrombocytopenia occurring within 5 – 10 days of administration of heparin is the most common clinical effect. The most severe complication of HIT is the occurrence of both venous and arterial thrombosis. Venous thrombosis can result in limb gangrene and the need for limb amputation.The diagnosis of HIT is based on clinical abnormalities including thrombocytopenia with or without thrombosis and the detection of antibodies to the PF4-heparin complex (termed PF4 dependant antibodies). There are two major types of assays for the detection of heparin dependant antibodies: functional assays and PF4 dependant antigen immunoassays. Functional assays include the serotonin release assay (SRA) and the heparin induced platelet activation assay (HIPA). Enzyme linked immunoassays (ELISAs) are the most frequently used PF4 dependent antigen immunoassay. Functional assays are technically difficult to perform and are considered to be complex specialty assays. ELISAs while not complex are not generally available on a STAT basis. There is a need for a simpler assay which retains or improves the sensitivity and specificity of the existing immunoassays that can be available on a STAT basis.GTI Diagnostics is developing a rapid test based on the proprietary technology used in GTI's PF4 Enhanced® ELISA. The PF4 Rapid test is a single use, semi-quantitative assay contained in a cartridge. It is designed to detect anti-PF4-heparin antibodies in human serum and/or plasma with a total assay time of 15 minutes. The assay uses only 5 μL of human serum and/or plasma along with a proprietary antigen and a proprietary fluorescent secondary antibody used for detection. The assay results are read using a fluorescent reader. A method comparison study was conducted which included an evaluation of 83 serum samples obtained from patients receiving heparin of which 36 were positive and 22 were negative in the PF4 Enhanced® assay. These samples were also tested in the PF4 Rapid Test assay. In addition 25 samples from normal individuals who were not receiving heparin were tested in both assays. Analysis of the data using a 2×2 table (shown below) resulted in a sensitivity of 100%, a specificity of 93.6% and an overall agreement of 96.4% of the PF4 Rapid Test compared to the PF4 Enhanced®.PF4 Enhanced® ELISAPositiveNegativeTotalPF4 Rapid TestPositive36339Negative04444Total364783Although HIT is a true clinicopathological syndrome, its diagnosis still rests primarily on clinical grounds since laboratory tests may not be available locally or may not be available in a sufficiently timely manner. Owing to the high risk of thrombosis associated with HIT, antithrombotic therapy with alternative anticoagulants should be started immediately when serologic assays confirm clinical suspicion. Readily available results, obtained from immunoassays for rapid detection of antibodies against PF4-heparin complexes, may be combined with the pretest estimation of clinical probability in order to exclude and/or confirm the diagnosis of HIT; therefore, assisting physicians in the time-sensitive clinical management of HIT. Disclosures:Ladvienka:GTI Diagnostics, Inc: Employment. Visentin:GTI Diagnostics, Inc: Employment. Chance:GTI Diagnostics, Inc: Employment.

An integrated microfluidic device for large-scale in situ click chemistry screening

An integrated microfluidic device has been developed to perform 1024 in situ click chemistry reactions in parallel using the bovine carbonic anhydrous II (bCAII) click chemistry system as a proof-of-concept study and a rapid hit identification approach using SPE purification and electrospray-ionization mass spectrometry, multiple reaction monitoring (MRM) analysis, all of which improves the sensitivity and throughput of the downstream analysis.

PhAST: Pharmacophore alignment search tool

We present a ligand-based virtual screening technique (PhAST) for rapid hit and lead structure searching in large compound databases. Molecules are represented as strings encoding the distribution of pharmacophoric features on the molecular graph. In contrast to other text-based methods using SMILES strings, we introduce a new form of text representation that describes the pharmacophore of molecules. This string representation opens the opportunity for revealing functional similarity between molecules by sequence alignment techniques in analogy to homology searching in protein or nucleic acid sequence databases. We favorably compared PhAST with other current ligand-based virtual screening methods in a retrospective analysis using the BEDROC metric. In a prospective application, PhAST identified two novel inhibitors of 5-lipoxygenase product formation with minimal experimental effort. This outcome demonstrates the applicability of PhAST to drug discovery projects and provides an innovative concept of sequence-based compound screening with substantial scaffold hopping potential.

Benzodioxoles: Novel Cannabinoid-1 Receptor Inverse Agonists for the Treatment of Obesity

The application of the evolutionary fragment-based de novo design tool TOPology Assigning System (TOPAS), starting from a known CB1R (CB-1 receptor) ligand, followed by further refinement principles, including pharmacophore compliance, chemical tractability, and drug likeness, allowed the identification of benzodioxoles as a novel CB1R inverse agonist series. Extensive multidimensional optimization was rewarded by the identification of promising lead compounds, showing in vivo activity. These compounds reversed the CP-55940-induced hypothermia in Naval Medical Research Institute (NMRI) mice and reduced body-weight gain, as well as fat mass, in diet-induced obese Sprague-Dawley rats. Herein, we disclose the tools and strategies that were employed for rapid hit identification, synthesis and generation of structure-activity relationships, ultimately leading to the identification of (+)-[( R)-2-(2,4-dichloride-phenyl)-6-fluoro-2-(4-fluoro-phenyl)-benzo[1,3]dioxol-5-yl]-morpholin-4-yl-methanone ( R)-14g . Biochemical, pharmacokinetic, and pharmacodynamic characteristics of ( R)-14g are discussed.

Rapid hit to lead evaluation of pyrazolo[3,4- d]pyrimidin-4-one as selective and orally bioavailable mGluR1 antagonists

Our HTS effort yielded a preferential mGluR1 pyrimidinone antagonist 1 with lead-like characteristics. Rapid hit to lead (HTL) study identified compounds with improved functional activity and selectivity such as 1b with little improvements in ADME properties. Addition of an aminosulfonyl group on the N-1 aromatic ring led to 2f, a compound with similar in vitro biochemical profiles as those of 1b but drastically improved in vitro ADME properties. These improvements were paralleled by rat PK study characterized by low clearance and quantitative bioavailability. Compound 2f represented a true lead-like molecule that is amenable for further lead optimization (LO) evaluation.

Finding polynomial roots: A fast algorithm convergent on the complex plane

AbstractAn algorithm is suggested which performs fast calculations of all the roots of a polynomial with maximal computer accuracy using, as the only primary information, the coefficients and the degree of the polynomial. The algorithm combines global as well as local convergences, i.e. it ensures a rapid hit into a small neighbourhood of a root for 2–3 iterations from any random initial approximation and cubic convergence within the neighbourhood. A modification of the method is given which allows the roots of entire functions to be found. A numerical comparison of the method with commonly used methods (Newton–Raphson, Bairstow–Newton, steepest descent) shows its advantages in speed, accuracy and stability both for real and complex polynomials.