Repositioning the Substrate Activity Screening (SAS) Approach as a Fragment‐Based Method for Identification of Weak Binders

Fragment‐based drug discovery (FBDD) has evolved into an established approach for “hit” identification. Typically, most applications of FBDD depend on specialised cost‐ and time‐intensive biophysical techniques. The substrate activity screening (SAS) approach has been proposed as a relatively cheap and straightforward alternative for identification of fragments for enzyme inhibitors. We have investigated SAS for the discovery of inhibitors of oncology target urokinase (uPA). Although our results support the key hypotheses of SAS, we also encountered a number of unreported limitations. In response, we propose an efficient modified methodology: “MSAS” (modified substrate activity screening). MSAS circumvents the limitations of SAS and broadens its scope by providing additional fragments and more coherent SAR data. As well as presenting and validating MSAS, this study expands existing SAR knowledge for the S1 pocket of uPA and reports new reversible and irreversible uPA inhibitor scaffolds.     

Integration of Multiple Analytical and Computational Tools for the Discovery of High‐Potency Enzyme Inhibitors from Herbal Medicines

Herbal medicines (HMs) are an important source of drugs. In this study, an efficient strategy integrating ultrafiltration LC–MS, microplate bioassays, and molecular docking was proposed to screen high‐potency enzyme inhibitors from HMs. Using this strategy, the structure–activity relationships (SARs) including binding‐affinity‐based SAR, enzymatic‐activity‐based SAR, and structural‐complementarity‐based SAR of compounds in an HM can be analyzed to provide abundant information for drug discovery. A prominent advantage of the approach is that it offers a multidimensional perspective to understand enzyme–ligand interactions, which could help to avoid false‐positive screening results brought by a single method. By using xanthine oxidase (XOD) as an illustrative case, two types of potent XOD inhibitors, including flavones and coumarins, were successfully screened out from an HM of Ginkgo biloba. The study is expected to set a solid foundation for multidisciplinary cooperation in drug discovery.     

Fragment‐Based Discovery of 5‐Arylisatin‐Based Inhibitors of Matrix Metalloproteinases 2 and 13

Matrix metalloproteinases (MMPs) are well‐established targets for several pathologies. In particular, MMP‐2 and MMP‐13 play a prominent role in cancer progression. In this study, a structure‐based screening campaign was applied to prioritize metalloproteinase‐oriented fragments. This computational model was applied to a representative fragment set from the publically available EDASA Scientific compound library. These fragments were prioritized, and the top‐ranking hits were tested in a biological assay to validate the model. Two scaffolds showed consistent activity in the assay, and the isatin‐based compounds were the most interesting. These latter fragments have significant potential as tools for the design and realization of novel MMP inhibitors. In addition to their micromolar activity, the chemical synthesis affords flexible and creative access to their analogues.     

Alzheimer’s Disease: Identification and Development of β‐Secretase (BACE‐1) Binding Fragments and Inhibitors by Dynamic Ligation Screening (DLS)

The application of dynamic ligation screening (DLS), a methodology for fragment‐based drug discovery (FBDD), to the aspartic protease β‐secretase (BACE‐1) is reported. For this purpose, three new fluorescence resonance energy transfer (FRET) substrates were designed and synthesized. Their kinetic parameters (V_max, K_M, and k_cat) were determined and compared with a commercial substrate. Secondly, a peptide aldehyde was designed as a chemically reactive inhibitor (CRI) based on the Swedish mutation substrate sequence. Incubation of this CRI with the protease, a FRET substrate, and one amine per well taken from an amine library, which was assembled by a maximum common substructure (MCS) approach, revealed the fragment 3‐(3‐aminophenyl)‐2H‐chromen‐2‐one ( 1 ) to be a competitive BACE‐1 inhibitor that enhanced the activity of the CRI. Irreversibly formed fragment combination products of 1 with the initial peptide sequence were active and confirmed the targeting of the active site through the ethane‐1,2‐diamine isostere. Finally, structure‐assisted combination of fragment 1 with secondary fragments that target the S1 site in hit optimization yielded novel, entirely fragment‐based BACE‐1 inhibitors with up to 30‐fold improved binding affinity. Interactions with the protein were explained by molecular modeling studies, which indicate that the new fragment combinations interact with the catalytic aspartic acid dyad, as well as with the adjacent binding sites required for potency.     

NMR Fragment Screening Hit Induces Plasticity of BRD7/9 Bromodomains

The complex biology associated with inhibition of bromodomain and extra‐terminal (BET) domains by chemical probes has attracted increasing attention, and there is a need to identify non‐BET bromodomain (BD) inhibitors. Several potent inhibitors of the BRD9 BD have recently been discovered, with anticancer and anti‐inflammation activity. However, its paralogue, BRD7 BD, remains unexploited. Here, we identified new chemotypes targeting BRD7 BD by using NMR fragment‐based screening. BRD7/9 BDs exhibit similar patterns of chemical‐shift perturbation upon the titration of hit compound 1 . The crystal structure revealed that 1 repels the Y222 group of BRD9 BD in a similar way to that for butyryllysine, but not acetyllysine and known inhibitors. Hit 1 induced less rearrangement of residue F161 of BRD9 BD than acetyllysine, butyryllysine, and crotonyllysine. Our study provides structural insight into a new generation of butyryllysine mimics for probing the function of BRD7/9 BD.     

Fragment‐Based Phenotypic Lead Discovery: Cell‐Based Assay to Target Leishmaniasis

A rapid and practical approach for the discovery of new chemical matter for targeting pathogens and diseases is described. Fragment‐based phenotypic lead discovery (FPLD) combines aspects of traditional fragment‐based lead discovery (FBLD), which involves the screening of small‐molecule fragment libraries to target specific proteins, with phenotypic lead discovery (PLD), which typically involves the screening of drug‐like compounds in cell‐based assays. To enable FPLD, a diverse library of fragments was first designed, assembled, and curated. This library of soluble, low‐molecular‐weight compounds was then pooled to expedite screening. Axenic cultures of Leishmania promastigotes were screened, and single hits were then tested for leishmanicidal activity against intracellular amastigote forms in infected murine bone‐marrow‐derived macrophages without evidence of toxicity toward mammalian cells. These studies demonstrate that FPLD can be a rapid and effective means to discover hits that can serve as leads for further medicinal chemistry purposes or as tool compounds for identifying known or novel targets.     

Identification of Highly Potent Protein Kinase C‐Related Kinase 1 Inhibitors by Virtual Screening,Binding Free Energy Rescoring,and in vitro Testing

Despite the considerable interest in protein kinase C‐related kinase 1 (PRK1) as a target in cancer research, there is still a lack of PRK1 inhibitors with suitable selectivity profiles and physicochemical properties. To identify new PRK1 inhibitors we applied a virtual screening approach, which combines ensemble docking, minimization of the protein–ligand complex, binding free energy calculations, and application of quantitative structure–activity relationship (QSAR) models for predicting in vitro activity. The developed approach was then applied in a prospective manner to screen available libraries of kinase inhibitors from Selleck and GlaxoSmithKline (GSK). Compounds that showed favorable prediction were then tested in vitro for PRK1 inhibition. Some of the hits were found to inhibit PRK1 in the low‐nanomolar range. Three in vitro hits were additionally tested in a mass‐spectrometry‐based cellular kinase profiling assay to examine selectivity. Our findings show that nanomolar and drug‐like inhibitors can be identified by the virtual screening approach presented herein. The identified inhibitors are valuable tools for gaining a better understanding of PRK1 inhibition, and the identified hits can serve as starting points for further chemical optimization.     

Synergistic Inhibitor Binding to the Papain‐Like Protease of Human SARS Coronavirus: Mechanistic and Inhibitor Design Implications

We previously developed two potent chemical classes that inhibit the essential papain‐like protease (PLpro) of severe acute respiratory syndrome coronavirus. In this study, we applied a novel approach to identify small fragments that act synergistically with these inhibitors. A fragment library was screened in combination with four previously developed lead inhibitors by fluorescence‐based enzymatic assays. Several fragment compounds synergistically enhanced the inhibitory activity of the lead inhibitors by approximately an order of magnitude. Surface plasmon resonance measurements showed that three fragments bind specifically to the PLpro enzyme. Mode of inhibition, computational solvent mapping, and molecular docking studies suggest that these fragments bind adjacent to the binding site of the lead inhibitors and further stabilize the inhibitor‐bound state. We propose potential next‐generation compounds based on a computational fragment‐merging approach. This approach provides an alternative strategy for lead optimization for cases in which direct co‐crystallization is difficult.     

Active Site Mapping of Human Cathepsin F with Dipeptide Nitrile Inhibitors

Cleavage of the invariant chain is the key event in the trafficking pathway of major histocompatibility complex class II. Cathepsin S is the major processing enzyme of the invariant chain, but cathepsin F acts in macrophages as its functional synergist which is as potent as cathepsin S in invariant chain cleavage. Dedicated low‐molecular‐weight inhibitors for cathepsin F have not yet been developed. An active site mapping with 52 dipeptide nitriles, reacting as covalent–reversible inhibitors, was performed to draw structure–activity relationships for the non‐primed binding region of human cathepsin F. In a stepwise process, new compounds with optimized fragment combinations were designed and synthesized. These dipeptide nitriles were evaluated on human cysteine cathepsins F, B, L, K and S. Compounds 10 (N‐(4‐phenylbenzoyl)‐leucylglycine nitrile) and 12 (N‐(4‐phenylbenzoyl)leucylmethionine nitrile) were found to be potent inhibitors of human cathepsin F, with K_i values <10 nM . With all dipeptide nitriles from our study, a 3D activity landscape was generated to visualize structure–activity relationships for this series of cathepsin F inhibitors.     

Using a Fragment‐Based Approach To Target Protein–Protein Interactions

The ability to identify inhibitors of protein–protein interactions represents a major challenge in modern drug discovery and in the development of tools for chemical biology. In recent years, fragment‐based approaches have emerged as a new methodology in drug discovery; however, few examples of small molecules that are active against chemotherapeutic targets have been published. Herein, we describe the fragment‐based approach of targeting the interaction between the tumour suppressor BRCA2 and the recombination enzyme RAD51; it makes use of a screening pipeline of biophysical techniques that we expect to be more generally applicable to similar targets. Disruption of this interaction in vivo is hypothesised to give rise to cellular hypersensitivity to radiation and genotoxic drugs. We have used protein engineering to create a monomeric form of RAD51 by humanising a thermostable archaeal orthologue, RadA, and used this protein for fragment screening. The initial fragment hits were thoroughly validated biophysically by isothermal titration calorimetry (ITC) and NMR techniques and observed by X‐ray crystallography to bind in a shallow surface pocket that is occupied in the native complex by the side chain of a phenylalanine from the conserved FxxA interaction motif found in BRCA2. This represents the first report of fragments or any small molecule binding at this protein–protein interaction site.     

Virtual Fragment Screening Identification of a Quinoline‐5,8‐dicarboxylic Acid Derivative as a Selective JMJD3 Inhibitor

The quinoline‐5,8 dicarboxylic acid scaffold has been identified by a fragment‐based approach as new potential lead compound for the development of JMJD3 inhibitors. Among them, 3‐(2,4‐dimethoxypyrimidin‐5‐yl)quinoline‐5,8‐dicarboxylic acid (compound 3 ) shows low micromolar inhibitory activity against Jumonji domain‐containing protein 3 (JMJD3). The experimental evaluation of inhibitory activity against seven related isoforms of JMJD3 highlighted an unprecedented selectivity toward the biological target of interest.     

Nano‐sized silica supported Me2Si(Ind)2ZrCl2/MAO catalyst for ethylene polymerization

Nano‐sized and micro‐sized silica particles were used to support a zirconocene catalyst [racemic‐dimethylsilbis(1‐indenyl)zirconium dichloride], with methylaluminoxane as a cocatalyst. The resulting catalyst was used to catalyze the polymerization of ethylene in the temperature range of 40–70°C. Polyethylene samples produced were characterized with scanning electron microscopy (SEM), X‐ray diffraction (XRD), differential scanning calorimetry (DSC), and gel permeation chromatography (GPC). Nano‐sized catalyst exhibited better ethylene polymerization activity than micro‐sized catalyst. At the optimum temperature of 60°C, nano‐sized catalyst's activity was two times the micro‐sized catalyst's activity. Polymers obtained with nano‐sized catalyst had higher molecular weight (based on GPC measurements) and higher crystallinity (based on XRD and DSC measurements) than those obtained with micro‐sized catalyst. The better performances of nano‐sized catalyst were attributed to its large external surface area and its absence of internal diffusion resistance. SEM indicated that polymer morphology contained discrete tiny particles with thin long fiberous interlamellar links. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2011     

Screening tests for the evaluation of nanoparticle titania photocatalysts

BACKGROUND: Nano‐sized titanium dioxide has potential as a photocatalyst, and doped variants may have different photocatalytic properties. Nano‐titanias with a wide range of dopants and compositions can be prepared using continuous hydrothermal flow synthesis (CHFS), but when many samples are made, a large‐scale screening test is required to investigate their properties. A range of doped nano‐titanias were prepared using a CHFS route, and investigated as powders using a range of photocatalytic test methods. These tests included decolourization of methylene blue (in the presence of oxygen), partial oxidation of a simple alcohol (propan‐2‐ol) and the degradation of aqueous solutions of dichloroacetic acid. The practicality of the tests for large‐scale screening was considered, and the test results were cross‐correlated to see if any of them gave similar ranking for activity of the photocatalysts. RESULTS: Two of the tests, namely DCA degradation and propan‐2‐ol, gave similar rank ordering for the nanopowders, while the MB decolourization results did not suggest a strong correlation with any other test. The addition of metal dopants was observed to produce varying results between different dopants and tests. CONCLUSIONS: Two of the tests, DCA degradation and MB decolourization in visible light, were recommended for further use as screening tests. Copyright © 2009 Society of Chemical Industry     

Synthetic Indolactam V Analogues as Inhibitors of PAR2‐Induced Calcium Mobilization in Triple‐Negative Breast Cancer Cells

Human proteinase‐activated receptor 2 (PAR2), a transmembrane G‐protein‐coupled receptor (GPCR), is an attractive target for a novel anticancer therapy, as it plays a critical role in cell migration and invasion. Selective PAR2 inhibitors therefore have potential as anti‐metastatic drugs. Knowing that the natural product teleocidin A2 is able to inhibit PAR2 in tumor cells, the goal of the present study was to elaborate structure–activity relationships and to identify potent PAR2 inhibitors with lower activity against the adverse target, protein kinase C (PKC). For this purpose, an efficient gram‐scale total synthesis of indolactam V (i.e., the parent structure of all teleocidins) was developed, and a library of derivatives was prepared. Some compounds were indeed found to exhibit high potency as PAR2 inhibitors at low nanomolar concentrations with improved selectivity (relative to teleocidin A2). The pseudopeptidic fragment bridging the C3 and C4 positions of the indole core proved to be essential for target binding, whereas activity and target selectivity depends on the substituents at N1 or C7. This study revealed novel derivatives that show high efficacy in PAR2 antagonism combined with increased selectivity.     

Fragment Screening of Soluble Epoxide Hydrolase for Lead Generation—Structure‐Based Hit Evaluation and Chemistry Exploration

Soluble epoxide hydrolase (sEH) is involved in the regulation of many biological processes by metabolizing the key bioactive lipid mediator, epoxyeicosatrienoic acids. For the development of sEH inhibitors with improved physicochemical properties, we performed both a fragment screening and a high‐throughput screening aiming at an integrated hit evaluation and lead generation. Followed by a joint dose–response analysis to confirm the hits, the identified actives were then effectively triaged by a structure‐based hit‐classification approach to three prioritized series. Two distinct scaffolds were identified as tractable starting points for potential lead chemistry work. The oxoindoline series bind at the right‐hand side of the active‐site pocket with hydrogen bonds to the protein. The 2‐phenylbenzimidazole‐4‐sulfonamide series bind at the central channel with significant induced fit, which has not been previously reported. On the basis of the encouraging initial results, we envision that a new lead series with improved properties could be generated if a vector is found that could merge the cyclohexyl functionality of the oxoindoline series with the trifluoromethyl moiety of the 2‐phenylbenzimidazole‐4‐sulfonamide series.     

Small‐Molecule APOBEC3G DNA Cytosine Deaminase Inhibitors Based on a 4‐Amino‐1,2,4‐triazole‐3‐thiol Scaffold

APOBEC3G (A3G) is a single‐stranded DNA cytosine deaminase that functions in innate immunity against retroviruses and retrotransposons. Although A3G can potently restrict Vif‐deficient HIV‐1 replication by catalyzing excessive levels of G→A hypermutation, sublethal levels of A3G‐catalyzed mutation may contribute to the high level of HIV‐1 fitness and its incurable prognosis. To chemically modulate A3G catalytic activity with the goal of decreasing the HIV‐1 genomic mutation rate, we synthesized and biochemically evaluated a class of 4‐amino‐1,2,4‐triazole‐3‐thiol small‐molecule inhibitors identified by high‐throughput screening. This class of compounds exhibits low‐micromolar (3.9–8.2 μM ) inhibitory potency and remarkable specificity for A3G versus the related cytosine deaminase, APOBEC3A. Chemical modification of inhibitors, A3G mutational screening, and thiol reactivity studies implicate C321, a residue proximal to the active site, as the critical A3G target for this class of molecules.     

Preparation of bitter taste masked cetirizine dihydrochloride/β-cyclodextrin inclusion complex by supercritical antisolvent (SAS) process

Rapid-disintegrating tablets (RDT) provide many advantages, such as rapid onset of action and assisting those patients who have difficulty swallowing. An important consideration in the formulation of RDT is masking the bitter taste of the drug to ensure patient compliance. The purpose of this study was to evaluate the possibility of inclusion complexation as a means of formulating taste masked cetirizine dihydrochloride (CTZ) rapid-disintegrating tablets. The inclusion complex between CTZ and β-cyclodextrin (β-CD) was prepared using a supercritical antisolvent (SAS) process, where dimethylsulfoxide (DMSO) was used as a liquid solvent and carbon dioxide (CO₂) as a supercritical antisolvent.Compared to large, irregular shaped products of freeze-drying method, small, spherically shaped, uniformly sized CTZ/β-CD inclusion complex products were successfully prepared by the SAS process. Concerning the structure of the complex, space conformation of the phenyl ring and chlorophenyl ring of CTZ in the β-CD hydrophobic cavity was confirmed by nuclear magnetic resonance spectroscopy (¹H NMR) and two-dimensional rotating frame overhauser effect spectroscopy (2D ROESY) studies. The obtained inclusion complex products prepared by both freeze-drying method and SAS process have the same efficacy in regards to dissolution characteristics and show the effective taste masking as compared to pure CTZ and CTZ/β-CD physical mixtures. In addition, the resulting products prepared by SAS process have negligible amount of residual solvent.     

3D QSAR pharmacophore modeling, in silico screening, and density functional theory (DFT) approaches for identification of human chymase inhibitors

Human chymase is a very important target for the treatment of cardiovascular diseases. Using a series of theoretical methods like pharmacophore modeling, database screening, molecular docking and Density Functional Theory (DFT) calculations, an investigation for identification of novel chymase inhibitors, and to specify the key factors crucial for the binding and interaction between chymase and inhibitors is performed. A highly correlating (r = 0.942) pharmacophore model (Hypo1) with two hydrogen bond acceptors, and three hydrophobic aromatic features is generated. After successfully validating "Hypo1", it is further applied in database screening. Hit compounds are subjected to various drug-like filtrations and molecular docking studies. Finally, three structurally diverse compounds with high GOLD fitness scores and interactions with key active site amino acids are identified as potent chymase hits. Moreover, DFT study is performed which confirms very clear trends between electronic properties and inhibitory activity (IC(50)) data thus successfully validating "Hypo1" by DFT method. Therefore, this research exertion can be helpful in the development of new potent hits for chymase. In addition, the combinational use of docking, orbital energies and molecular electrostatic potential analysis is also demonstrated as a good endeavor to gain an insight into the interaction between chymase and inhibitors.     

Discovery of Plasmepsin Inhibitors by Fragment‐Based Docking and Consensus Scoring

Plasmepsins (PMs) are essential proteases of the plasmodia parasites and are therefore promising targets for developing drugs against malaria. We have discovered six inhibitors of PM II by high‐throughput fragment‐based docking of a diversity set of ～40 000 molecules, and consensus scoring with force field energy functions. Using the common scaffold of the three most active inhibitors (IC₅₀=2–5 μM ), another seven inhibitors were identified by substructure search. Furthermore, these 13 inhibitors belong to at least three different classes of compounds. The in silico approach was very effective since a total of 13 active compounds were discovered by testing only 59 molecules in an enzymatic assay. This hit rate is about one to two orders of magnitude higher than those reported for medium‐ and high‐throughput screening techniques in vitro. Interestingly, one of the inhibitors identified by docking was halofantrine, an antimalarial drug of unknown mechanism. Explicit water molecular dynamics simulations were used to discriminate between two putative binding modes of halofantrine in PM II.     

Identification of Novel Fragments Binding to the PDZ1-2 Domain of PSD-95

Inhibition of PSD-95 has emerged as a promising strategy for the treatment of ischemic stroke, as shown with peptide-based compounds that target the PDZ domains of PSD-95. In contrast, developing potent and drug-like small molecules against the PSD-95 PDZ domains has so far been unsuccessful. Here, we explore the druggability of the PSD-95 PDZ1-2 domain and use fragment screening to investigate if this protein is prone to binding small molecules. We screened 2500 fragments by fluorescence polarization (FP) and validated the hits by surface plasmon resonance (SPR), including an inhibition counter-test, and found four promising fragments. Three ligand efficient fragments were shown by ¹H,¹⁵N HSQC NMR to bind in the small hydrophobic P⁰ pockets of PDZ1-2, and one of them underwent structure-activity relationship (SAR) studies. Overall, we demonstrate that fragment screening can successfully be applied to PDZ1-2 of PSD-95 and disclose novel fragments that can serve as starting points for optimization towards small-molecule PDZ domain inhibitors.