Hit Validation Research Articles

Whole genome CRISPR screening strategy to identify genes contributing to SARS-CoV-2 spike and VSV-G mediated entry.

Understanding the cellular host factors that promote and inhibit viral entry is important for identifying viral countermeasures. CRISPR whole-genome screens can be used to rapidly discover host factors that contribute to or impair viral entry. However, when using live viruses and cellular lethality for selection, these screens can identify an overwhelming number of genes without specificity for the stage of the viral infection cycle. New screening methods are needed to identify host machinery contributing to specific steps of viral infection. Here, we developed a CRISPR whole-genome screen and counter-screen strategy based on a pseudoviral platform that allowed identification of genes specific to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike and vesicular stomatitis virus glycoprotein (VSV-G) mediated entry.Screening of SARS-CoV-2 spike and VSV-G on the same lentiviral pseudovirus allowed the identification of entry-specific genes relative to genes associated with retro-transcription, integration, and reporter expression from the lentiviral pseudovirus. Second, a Cre-Gag fusion protein packaged into the pseudovirus was used to bypass retro-transcription and integration by directly activating a floxed fluorescent protein reporter upon entry reduced the number of gene hits and increase specificity for viral entry.Our approach correctly identified SARS-CoV-2 and VSV-G receptors ACE2 and low-density lipoprotein receptors, respectively, and distinguished genes associated with retroviral reporter expression from envelope-mediated entry. Moreover, the CRE-Gag fusion/flox reporter increased the screen specificity for viral entry-associated genes. Validation of a few hits demonstrates that this approach distinguishes envelope-specific host factors from genes affecting reporter expression.Overall, this approach provides a new strategy for identifying host genes influencing viral entry without the confounding complexity of live-viral screens which produce long gene lists associated with all aspects of viral pathogenesis and replication.

Fortuitous In Vitro Compound Degradation Produces a Tractable Hit against Mycobacterium tuberculosis Dethiobiotin Synthetase: A Cautionary Tale of What Goes In Does Not Always Come Out.

We previously reported potent ligands and inhibitors of Mycobacterium tuberculosis dethiobiotin synthetase (MtDTBS), a promising target for antituberculosis drug development (Schumann et al., ACS Chem Biol. 2021, 16, 2339-2347); here, the unconventional origin of the fragment compound they were derived from is described for the first time. Compound 1 (9b-hydroxy-6b,7,8,9,9a,9b-hexahydrocyclopenta[3,4]cyclobuta[1,2-c]chromen-6(6aH)-one), identified by an in silico fragment screen, was subsequently shown by surface plasmon resonance to have dose-responsive binding (KD = 0.6 mM). Clear electron density was revealed in the DAPA substrate binding pocket when 1 was soaked into MtDTBS crystals, but the density was inconsistent with the structure of 1. Here, we show that the lactone of 1 hydrolyzes to a carboxylic acid (2) under basic conditions, including those of the crystallography soak, with a subsequent ring opening of the component cyclobutane ring forming a cyclopentylacetic acid (3). Crystals soaked directly with authentic 3 produced an electron density that matched that of crystals soaked with presumed 1, confirming the identity of the bound ligand. The synthetic utility of fortuitously formed 3 enabled the subsequent compound development of nanomolar inhibitors. Our findings represent an example of chemical modification within drug discovery assays and demonstrate the value of high-resolution structural data in the fragment hit validation process.

Fragment Screening and Fast Micromolar Detection on a Benchtop NMR Spectrometer Boosted by Photoinduced Hyperpolarization.

Fragment-based drug design is a well-established strategy for rational drug design, with nuclear magnetic resonance (NMR) on high-field spectrometers as the method of reference for screening and hit validation. However, high-field NMR spectrometers are not only expensive, but require specialized maintenance, dedicated space, and depend on liquid helium cooling which became critical over the recurring global helium shortages. We propose an alternative to high-field NMR screening by applying the recently developed approach of fragment screening by photoinduced hyperpolarized NMR on a cryogen-free 80 MHz benchtop NMR spectrometer yielding signal enhancements of up to three orders in magnitude. It is demonstrated that it is possible to discover new hits and kick-off drug design using a benchtop NMR spectrometer at low micromolar concentrations of both protein and ligand. The approach presented performs at higher speed than state-of-the-art high-field NMR approaches while exhibiting a limit of detection in the nanomolar range. Photoinduced hyperpolarization is known to be inexpensive and simple to be implemented, which aligns greatly with the philosophy of benchtop NMR spectrometers. These findings open the way for the use of benchtop NMR in near-physiological conditions for drug design and further life science applications.

Fragment‐Screening und schnelle mikromolare Detektion mit einem Benchtop‐NMR‐Spektrometer ermöglicht durch photoinduzierte Hyperpolarisation

AbstractFragmentbasiertes Wirkstoffdesign ist eine gut etablierte Strategie für rationales Arzneimitteldesign, wobei die Kernspinresonanzspektroskopie (NMR) auf Hochfeldspektrometern als Referenzmethode für das Screening und die Hit‐Validierung dient. Hochfeld‐NMR‐Spektrometer sind jedoch nicht nur teuer, sondern erfordern auch eine spezielle Wartung, einen speziellen Raum und sind auf die Kühlung mit flüssigem Helium angewiesen, was angesichts der wiederkehrenden weltweiten Heliumknappheit kritisch geworden ist. Wir schlagen eine Alternative zum Hochfeld‐NMR‐Screening vor, indem wir den kürzlich entwickelten Ansatz des Fragment‐Screenings durch photoinduzierte hyperpolarisierte NMR auf einem kryogenfreien 80‐MHz‐Benchtop‐NMR‐Spektrometer anwenden, der Signalverstärkungen von bis zu drei Größenordnungen ermöglicht. Es wird gezeigt, dass es möglich ist, mit einem Benchtop‐NMR‐Spektrometer bei niedrigen mikromolaren Konzentrationen sowohl von Proteinen als auch von Liganden neue Hits zu entdecken und die Entwicklung von Medikamenten einzuleiten. Der vorgestellte Ansatz arbeitet mit höherer Geschwindigkeit als moderne Hochfeld‐NMR‐Ansätze und weist eine Nachweisgrenze im nanomolaren Bereich auf. Die photoinduzierte Hyperpolarisation ist bekanntlich kostengünstig und einfach zu implementieren, was der Philosophie von Benchtop‐NMR‐Spektrometern sehr entgegenkommt. Diese Ergebnisse ebnen den Weg für den Einsatz von Benchtop‐NMRunter nahezu physiologischen Bedingungen für die Entwicklung von Arzneimitteln und weitere Life‐Science‐Anwendungen.

Small Molecule Activation of NAPE-PLD Enhances Efferocytosis by Macrophages.

N-Acyl-phosphatidylethanolamine hydrolyzing phospholipase D (NAPE-PLD) is a zinc metallohydrolase that hydrolyzes N-acyl-phosphatidylethanolamines (NAPEs) to form N-acyl-ethanolamines (NAEs) and phosphatidic acid. Several lines of evidence suggest that reduced NAPE-PLD activity could contribute to cardiometabolic diseases. For instance, NAPEPLD expression is reduced in human coronary arteries with unstable atherosclerotic lesions, defective efferocytosis is implicated in the enlargement of necrotic cores of these lesions, and NAPE-PLD products such as palmitoylethanolamide and oleoylethanolamide have been shown to enhance efferocytosis. Thus, enzyme activation mediated by a small molecule may serve as a therapeutic treatment for cardiometabolic diseases. As a proof-of-concept study, we sought to identify small molecule activators of NAPE-PLD. High-throughput screening followed by hit validation and primary lead optimization studies identified a series of benzothiazole phenylsulfonyl-piperidine carboxamides that variably increased activity of both mouse and human NAPE-PLD. From this set of small molecules, two NAPE-PLD activators (VU534 and VU533) were shown to increase efferocytosis by bone-marrow derived macrophages isolated from wild-type mice, while efferocytosis was significantly reduced in Napepld-/- BMDM or after Nape-pld inhibition. Together, these studies demonstrate an essential role for NAPE-PLD in the regulation of efferocytosis and the potential value of NAPE-PLD activators as a strategy to treat cardiometabolic diseases.

Identification of Azelastine and Carvedilol as Cholinesterase Inhibitors via Structure‐Based Virtual Screening of FDA‐approved Drugs

AbstractThe structure‐based virtual screening (SBVS) has gained immense importance in early drug discovery. Herein, we report the SBVS‐driven identification of new cholinesterase inhibitors from a library of FDA‐approved small molecule drugs (n=1760). The in vitro validation of top SBVS hits provided azelastine, dronedarone, and iloperidone as acetylcholinesterase (AChE) inhibitors with IC50 values of 9.2, 18.2, and 23.0 μM, respectively. The in vitro screening of top actives in the butyrylcholinesterase (BChE) inhibition assay provided carvedilol as a potent BChE inhibitor with an IC50 of 0.8 μM. Azelastine also inhibits BChE with IC50 of 4.89 μM, indicating its dual ChE inhibition activity. Azelastine and carvedilol also inhibit the self‐aggregation of Aβ1–42 with IC50 values of 4.6 and 2.2 μM, respectively. Both drugs cross blood‐brain barrier (BBB), as indicated by the parallel artificial membrane permeation assay. Results presented herein warrant exploring the repurposing potential of azelastine and carvedilol for Alzheimer's disease.

A DNA-encoded chemical library based on chiral 4-amino-proline enables stereospecific isozyme-selective protein recognition.

DNA-encoded chemical libraries (DELs) consist of large chemical compound collections individually linked to DNA barcodes, facilitating pooled construction and screening. However, screening campaigns often fail if the molecular arrangement of the building blocks is not conducive to an efficient interaction with a protein target. Here we postulated that the use of rigid, compact and stereo-defined central scaffolds for DEL synthesis may facilitate the discovery of very specific ligands capable of discriminating between closely related protein targets. We synthesized a DEL comprising 3,735,936 members, featuring the four stereoisomers of 4-aminopyrrolidine-2-carboxylic acid as central scaffolds. The library was screened in comparative selections against pharmaceutically relevant targets and their closely related protein isoforms. Hit validation results revealed a strong impact of stereochemistry, with large affinity differences between stereoisomers. We identified potent isozyme-selective ligands against multiple protein targets. Some of these hits, specific to tumour-associated antigens, demonstrated tumour-selective targeting in vitro and in vivo. Collectively, constructing DELs with stereo-defined elements contributed to high library productivity and ligand selectivity.

Investigation of enzalutamide, docetaxel, and cabazitaxel resistance in the castration resistant prostate cancer cell line C4 using genome-wide CRISPR/Cas9 screening

Enzalutamide, docetaxel, and cabazitaxel treatment resistance is a major problem in metastatic castration resistant prostate cancer (mCRPC), but the underlying genetic determinants are poorly understood. To identify genes that modulate treatment response to these drugs, we performed three genome-wide CRISPR/Cas9 knockout screens in the mCRPC cell line C4. The screens identified seven candidates for enzalutamide (BCL2L13, CEP135, E2F4, IP6K2, KDM6A, SMS, and XPO4), four candidates for docetaxel (DRG1, LMO7, NCOA2, and ZNF268), and nine candidates for cabazitaxel (ARHGAP11B, DRG1, FKBP5, FRYL, PRKAB1, RP2, SMPD2, TCEA2, and ZNF585B). We generated single-gene C4 knockout clones/populations for all genes and could validate effect on treatment response for five genes (IP6K2, XPO4, DRG1, PRKAB1, and RP2). Altered enzalutamide response upon IP6K2 and XPO4 knockout was associated with deregulation of AR, mTORC1, and E2F signaling, and deregulated p53 signaling (IP6K2 only) in C4 mCRPC cells. Our study highlights the necessity of performing individual validation of candidate hits from genome-wide CRISPR screens. Further studies are needed to assess the generalizability and translational potential of these findings.

Abstract B073: Inhibiting prostate cancer by targeting the metabolic mevalonate pathway

Abstract Background: A major challenge in the clinical management of prostate cancer (PCa) is inhibiting progression to lethal castrate-resistant PC (CRPC). Deregulated activity of mevalonate (MVA), cholesterol biosynthetic pathway is a recognized hallmark of PCa cells. Statins are potent inhibitors of this metabolic pathway that have been used for decades in the control of hypercholesterolemia. Statins have recently been shown to have anti-PCa activity, however statin treatment triggers a feedback response that restores the MVA pathway, which reduces statin efficacy and contributes to resistance. This restorative feedback loop is controlled by the transcriptional activity of sterol regulatory-element binding protein (SREBP), which primarily induces fatty acid biosynthesis and MVA pathway genes. We have recently identified the anti-platelet agent dipyridamole (DP) as an inhibitor of the statin-induced SREBP-mediated feedback response. However, DP is not SREBP-specific and given its anti-platelet activity, may not be suitable for every cancer patient. Thus, our goal was to identify additional drugs that potentiate the pro-apoptotic activity of statins, which can be used to treat PCa patients. Methods: Two independent, yet complimentary strategies were used. The first focused on performing an in silico analysis to identify drugs that had similar properties to DP at the level of drug structure, molecular perturbations and cell line sensitivity. The second strategy involved a high-content imaging analysis of 1508 FDA approved drugs, which was performed in LNCaP (relatively statin insensitive and feedback competent) and PC3 cells (statin sensitive and feedback incompetent). Cells were treated with a sub-lethal dose of fluvastatin, the drugs or the fluvastatin-drug combination, then treated with apoptotic stains (TMRE, Annexin, Draq 5). Captured images were analyzed using a machine learning approach. Results: Validation of hits from the in silico MVA-DNF approach and high-content screening has identified several drugs that fulfill our criteria of potentiating statin-induced cell death in a feedback-dependent or feedback-independent manner. Interestingly, many show higher Z-scores compared to DP indicating their superior statin potentiation activity to drive PCa cell death. Moreover, a sub-set of these drug significantly inhibit statin-triggered expression of MVA pathway genes HMGCS1 and INSIG1 (p < 0.001) more potently than DP. Conclusions: We have detailed two successful strategies to identify drugs that inhibit SREBP activation in response to statin treatment. These statin-drug combinations represent an effective ‘one-two punch’ to inhibit CRPC progression. These novel inhibitors of SREBP activation potentiate statin at clinically relevant concentrations more potently than DP and have no effect on the platelet activity. Excitingly, many of these agents are FDA-approved and can be immediately used in combination with statins for the treatment of PCa. Overall, our research will lead to novel therapies to improve patient outcome. Citation Format: Diandra Zipinotti dos Santos, Mohamad Elbaz, Emily Branchard, Wiebke Schormann, David W. Andrews, Linda Z. Penn. Inhibiting prostate cancer by targeting the metabolic mevalonate pathway [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr B073.

Fragtory: Pharmacophore-Focused Design, Synthesis, and Evaluation of an sp3-Enriched Fragment Library.

Fragment-based drug discovery has played an important role in medicinal chemistry and pharmaceutical research. Despite numerous demonstrated successes, the limited diversity and overrepresentation of planar, sp2-rich structures in commercial libraries often hamper the full potential of this approach. Hence, the thorough design of screening libraries inevitably determines the probability for meaningful hits and subsequent structural elaboration. Against this background, we present the generation of an exclusive fragment library based on iterative entry nomination by a specifically designed computational workflow: "Fragtory". Following a pharmacophore diversity-driven approach, we used Fragtory in an interdisciplinary academic setting to guide both tailored synthesis efforts and the implementation of in-house compounds to build a curated 288-member library of sp3-enriched fragments. Subsequent NMR screens against a model protein and hit validation by protein crystallography led to the identification of structurally novel ligands that were further characterized by isothermal titration calorimetry, demonstrating the applicability of our experimental approach.

Abstract 2912: High-throughput screening and single-cell transcriptomics identify synergies between oncology drugs and natural killer cell immunotherapy

Abstract Background & Objective: Natural killer (NK) cell-based immunotherapies are emerging therapeutic approaches that aim to target malignant cells resistant to conventional treatments and T cell-based immunotherapies. Existing oncology drugs may enhance the anti-cancer function of NK cells, although large-scale high-throughput testing of NK cell-drug combinations has not been previously attempted. Our objective was to evaluate the potential of approved and investigational oncology drugs to synergize with NK cell-based immunotherapy in acute myeloid leukemia (AML), with the aim to discover both potentiating and inhibiting compounds. Methods: A high-throughput drug sensitivity and resistance screen including 528 oncology drugs was combined with expanded NK cells to evaluate their cytotoxicity against luciferase-expressing AML cells (MOLM-14). The most prominent drugs were investigated further with single-cell RNA sequencing to reveal underlying biological mechanisms. Results: Overall, 191 drugs had an inhibitory effect on cytotoxicity, 294 had no effect, and 43 had an enhancing effect. The most notable NK cell cytotoxicity-potentiating drugs were pevonedistat (NEDD8 inhibitor), daporinad (NAMPT inhibitor), and JAK inhibitors. These drugs also induced distinct changes in NK and target cell transcriptional profiles. When combined with NK cells, pevonedistat and daporinad induced an upregulation of HLA-E and CXCL10 in target cells. In addition, MYC and FLT3 proto-oncogenes were downregulated in target cells when combining NK cells with pevonedistat. Moreover, in NK cells, daporinad induced dysregulated expression of genes related to NK cell effector functions such as TYROBP, TXNIP and KLRC1. Treatment with JAK inhibitors downregulated MHC I expression on target cells, providing a putative mechanism for increased NK cell activity. Validation of key hits is ongoing in additional AML cell lines. Conclusion: We discovered novel drugs with both potentiating and inhibiting effects on NK cell cytotoxicity against AML cells in vitro. Our results demonstrate the potential of using a high-throughput framework for studying NK cell-drug interactions against malignant cells, while aiming to improve treatment for AML and other malignancies through combination immunotherapies. Citation Format: Jonas O. Bouhlal, Petra Nygren, Essi Laajala, Aleksandr Ianevski, Jay Klievink, Hanna Lähteenmäki, Khalid Saeed, Dean Lee, Tero Aittokallio, Olli Dufva, Satu Mustjoki. High-throughput screening and single-cell transcriptomics identify synergies between oncology drugs and natural killer cell immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2912.

Abstract 6089: Identification of novel YAP/TAZ pathway regulators in the triple-negative breast cancer cell line MDA-MB231 using single-cell CRISPR screening

Abstract The Hippo signaling cascade is a major pathway that integrates a broad spectrum of mechanosensory signals at the plasma membrane and regulates response via control of cell proliferation, self-renewal, differentiation, and apoptosis. Dysregulation of this pathway has been observed across a range of cancer types and results in an altered activity of its primary downstream effectors, the oncogenic transcription factors YAP/TAZ. For example, both germline and somatic loss-of-function mutations in the tumor suppressor gene NF2, a component of Hippo, induce hyperactivation of YAP/TAZ, transcriptional changes and ultimately result in tumor growth. The Hippo signaling pathway is an attractive target for drug discovery efforts, however, it is highly complex and still incompletely understood. Hence it is indispensable to get a deeper insight into the Hippo - YAP/TAZ signaling axis. To this end, we performed a genome-wide CRISPR knockout screen in the triple-negative breast cancer (TNBC) cell line MDA-MB231 (NF2LOF) expressing a YAP/TAZ reporter construct. We identified both negative and positive regulators of YAP/TAZ in breast cancer cells. In a second step, screening hits were further characterized in a focused single-cell CRISPR screen (Perturb-Seq), aiming at better understanding of the effects on YAP/TAZ activity regulation and downstream effects on gene expression. Here we present the technical details of our screening approaches and the results of perturbing known and novel regulators of YAP/TAZ on single cell level. We discuss the use of Perturb-Seq in the initial validation of hits from genome-wide screens and provide data that may serve as a basis for future drug discovery efforts, seeking for novel and effective treatments for triple-negative breast cancers and other malignancies with Hippo pathway alterations. Citation Format: Mareike Berlak, Zuzanna Makowska, Filippos Klironomos, Julia Kuehnlenz, Atanas Kamburov, Andreas Steffen, Martin Lange, Barbara Nicke, Ralf Lesche, Peter Staller, Charlotte Kopitz, Jan Naujoks. Identification of novel YAP/TAZ pathway regulators in the triple-negative breast cancer cell line MDA-MB231 using single-cell CRISPR screening [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6089.

High throughput screening of 0.5 Million compounds against CRAF using Alpha CETSAⓇ.

The cellular thermal shift assay (CETSA®) has increasingly been used in early drug discovery to provide a measure of cellular target engagement. Traditionally, CETSA has been employed for bespoke questions with small to medium throughput and has predominantly been applied during hit validation rather than in hit identification. Using a CETSA screen versus the kinase CRAF, we assessed 3 key questions: (1) technical feasibility - could the CETSA methodology technically be applied at truly high throughput scale? (2) relevance - could hits suitable for further optimisation be identified? (3) reliability - would the approach identify known chemical equity. Here, we describe the first large scale AlphaLISA SureFire based CETSA (Alpha CETSA) approach allowing us to screen a large library of almost 0.5 million compounds. We discuss the issues overcome in automating and executing the screen and describe the resulting screen output.

Evaluation of In Vitro and In Vivo Antiviral Activities of Vitamin D for SARS-CoV-2 and Variants

The COVID-19 pandemic has brought about unprecedented medical and healthcare challenges worldwide. With the continual emergence and spread of new COVID-19 variants, four drug compound libraries were interrogated for their antiviral activities against SARS-CoV-2. Here, we show that the drug screen has resulted in 121 promising anti-SARS-CoV-2 compounds, of which seven were further shortlisted for hit validation: citicoline, pravastatin sodium, tenofovir alafenamide, imatinib mesylate, calcitriol, dexlansoprazole, and prochlorperazine dimaleate. In particular, the active form of vitamin D, calcitriol, exhibits strong potency against SARS-CoV-2 on cell-based assays and is shown to work by modulating the vitamin D receptor pathway to increase antimicrobial peptide cathelicidin expression. However, the weight, survival rate, physiological conditions, histological scoring, and virus titre between SARS-CoV-2 infected K18-hACE2 mice pre-treated or post-treated with calcitriol were negligible, indicating that the differential effects of calcitriol may be due to differences in vitamin D metabolism in mice and warrants future investigation using other animal models.

Identification of Small-Molecule Inhibitors of the Salmonella FraB Deglycase Using a Live-Cell Assay.

Nontyphoidal salmonellosis is one of the most significant foodborne diseases in the United States and globally. There are no vaccines available for human use to prevent this disease, and only broad-spectrum antibiotics are available to treat complicated cases of the disease. However, antibiotic resistance is on the rise and new therapeutics are needed. We previously identified the Salmonella fraB gene, that mutation of causes attenuation of fitness in the murine gastrointestinal tract. The FraB gene product is encoded in an operon responsible for the uptake and utilization of fructose-asparagine (F-Asn), an Amadori product found in several human foods. Mutations in fraB cause an accumulation of the FraB substrate, 6-phosphofructose-aspartate (6-P-F-Asp), which is toxic to Salmonella. The F-Asn catabolic pathway is found only in the nontyphoidal Salmonella serovars, a few Citrobacter and Klebsiella isolates, and a few species of Clostridium; it is not found in humans. Thus, targeting FraB with novel antimicrobials is expected to be Salmonella specific, leaving the normal microbiota largely intact and having no effect on the host. We performed high-throughput screening (HTS) to identify small-molecule inhibitors of FraB using growth-based assays comparing a wild-type Salmonella and a Δfra island mutant control. We screened 224,009 compounds in duplicate. After hit triage and validation, we found three compounds that inhibit Salmonella in an fra-dependent manner, with 50% inhibitory concentration (IC50) values ranging from 89 to 150 μM. Testing these compounds with recombinant FraB and synthetic 6-P-F-Asp confirmed that they are uncompetitive inhibitors of FraB with Ki' (inhibitor constant) values ranging from 26 to 116 μM. IMPORTANCE Nontyphoidal salmonellosis is a serious threat in the United States and globally. We have recently identified an enzyme, FraB, that when mutated renders Salmonella growth defective in vitro and unfit in mouse models of gastroenteritis. FraB is quite rare in bacteria and is not found in humans or other animals. Here, we have identified small-molecule inhibitors of FraB that inhibit the growth of Salmonella. These could provide the foundation for a therapeutic to reduce the duration and severity of Salmonella infections.

Discovery of TRD‐93 as a novel DRAK2 inhibitor

AbstractDeath‐associated protein kinase‐related apoptosis‐inducing protein kinase 2 (DRAK2) has become a promising target for drug development. In search of novel and selective DRAK2 inhibitor motif, in vitro screen kinase assay was established performed using in‐house chemical libraries. After through hit triage procedure, N2‐(3,5‐dichlorophenyl)‐5‐fluoro‐N4‐methylpyrimidine‐2,4‐diamine (1) was selected as initial hit with structural novelty and drug‐likeness. During hit validation, structure–activity relationship of 1 was thoroughly disclosed and TRD‐93 was finally validated as hit for DRAK2 inhibition. TRD‐93 is small (mw = 290) but selectively potent to DRAK2 (IC50 = 0.16 μM) over other kinases including DAPK family kinases. Molecular binding model study of TRD‐93 to DRAK2 is also discussed.

Pharmacophore-Aided Virtual Screening and Molecular Dynamics Simulation Identifies TrkB Agonists for Treatment of CDKL5-Deficiency Disorders.

Therapeutic intervention in cyclin-dependent kinase-like 5 (CDKL5) deficiency disorders (CDDs) has remained a concern over the years. Recent advances into the mechanistic interplay of signalling pathways has revealed the role of deficient tropomyosin receptor kinase B (TrkB)/phospholipase C γ1 signalling cascade in CDD. Novel findings showed that in vivo administration of a TrkB agonist, 7,8-dihydroxyflavone (7,8-DHF), resulted in a remarkable reversal in the molecular pathologic mechanisms underlying CDD. Owing to this discovery, this study aimed to identify more potent TrkB agonists than 7,8-DHF that could serve as alternatives or combinatorial drugs towards effective management of CDD. Using pharmacophore modelling and multiple database screening, we identified 691 compounds with identical pharmacophore features with 7,8-DHF. Virtual screening of these ligands resulted in identification of at least 6 compounds with better binding affinities than 7,8-DHF. The in silico pharmacokinetic and ADMET studies of the compounds also indicated better drug-like qualities than those of 7,8-DHF. Postdocking analyses and molecular dynamics simulations of the best hits, 6-hydroxy-10-(2-oxo-1-azatricyclo[7.3.1.05,13]trideca-3,5(13),6,8-tetraen-3-yl)-8-oxa-13,14,16-triazatetracyclo[7.7.0.02,7.011,15]hexadeca-1,3,6,9,11,15-hexaen-5-one (PubChem: 91637738) and 6-hydroxy-10-(8-methyl-2-oxo-1H-quinolin-3-yl)-8-oxa-13,14,16-triazatetracyclo[7.7.0.02,7.011,15]hexadeca-1,3,6,9,11,15-hexaen-5-one (PubChem ID: 91641310), revealed unique ligand interactions, validating the docking findings. We hereby recommend experimental validation of the best hits in CDKL5 knock out models before consideration as drugs in CDD management.

Fragment-based screening by protein-detected NMR spectroscopy.

Fragment-based drug discovery (FBDD) identifies low molecular weight compounds that can be developed into ligands with high affinity and selectivity for therapeutic targets. Screening fragment libraries (<10,000 molecules) with biophysical techniques against macromolecules provides information about novel chemical spacesthat bind the macromolecule and scaffolds that can be modified to increase potency. A fragment-screening pipeline requires a standardized protocol for target selection, library assembly and maintenance, library screening, and hit validation to ensure hit integrity. Herein, the fundamental aspects of a fragment screening pipeline-focusing on protein-detected NMR data collection and analysis-are discussed in detail for researchers to use as a resource in their FBDD projects. Selected screening targets must undergo rigorous stability and buffer testing by NMR spectroscopy to ensure the protein structure is stable for the entire screen. Biophysical instrumentation that rapidly measures protein thermostability is helpful in buffer screening. Molecules in fragment libraries are analyzed computationally and physically, stored at appropriate temperatures, and multiplexed in well plates for library conservation. The screening protocol is streamlined using liquid handling robotics for sample preparation and customized Python scripts for protein-detected NMR data analysis. Molecules identified from the screen are titrated to determine their binding site(s) and Kd values and confirmed with an orthogonal biophysical assay. This detailed FBDD screening pipeline developed by the Program in Chemical Biology at the Medical College of Wisconsin has successfully screened many unrelated target proteins to identified novel molecules that selectively bind to these target proteins.

Efficiently driving protein-based fragment screening and lead discovery using two-dimensional NMR.

Fragment-based drug discovery (FBDD) and validation of small molecule binders using NMR spectroscopy is an established and widely used method in the early stages of drug discovery. Starting from a library of small compounds, ligand- or protein-observed NMR methods are employed to detect binders, typically weak, that become the starting points for structure-activity relationships (SAR) by NMR. Unlike the more frequently used ligand-observed 1D NMR techniques, protein-observed 2D 1H-15N or 1H-13C heteronuclear correlation (HSQC or HMQC) methods offer insights that include the mechanism of ligand engagement on the target and direct binding affinity measurements in addition to routine screening. We hereby present the development of a set of software tools within the MestReNova (Mnova) package for analyzing 2D NMR for FBDD and hit validation purposes. The package covers three main tasks: (1) unsupervised profiling of raw data to identify outlier data points to exclude in subsequent analyses; (2) batch processing of single-point spectra to identify and rank binders based on chemical shift perturbations or spectral peak intensity changes; and (3) batch processing of multiple titration series to derive binding affinities (KD) by tracing the changes in peak locations or measuring global spectral changes. Toward this end, we implemented and evaluated a set of algorithms for automated peak tracing, spectral binning, and variance analysis by PCA, and a new tool for spectral data intensity comparison using ECHOS. The accuracy and speed of the tools are demonstrated on 2D NMR binding data collected on ligands used in the development of potential inhibitors of the anti-apoptotic MCL-1 protein.

High-Throughput Screening to Identify Modulators of Sarcospan.

High-throughput screening enables the discovery of disease-modifying small molecules. Here, we describe the development of a scalable, cell-based assay to screen for small molecules that modulate sarcospan for the treatment of Duchenne muscular dystrophy. We detail the hit validation pipeline, which includes secondary screening, gene/protein quantification, and an in vitro membrane stability assay.