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CRISPR–Cas genome-editing nucleases hold substantial promise for developing human therapeutic applications1–6but identifying unwanted off-target mutations is important for clinical translation7. A well-validated method that can reliably identify off-targets in vivo has not been described to date, which means it is currently unclear whether and how frequently these mutations occur. Here we describe ‘verification of in vivo off-targets’ (VIVO), a highly sensitive strategy that can robustly identify the genome-wide off-target effects of CRISPR–Cas nucleases in vivo. We use VIVO and a guide RNA deliberately designed to be promiscuous to show that CRISPR–Cas nucleases can induce substantial off-target mutations in mouse livers in vivo. More importantly, we also use VIVO to show that appropriately designed guide RNAs can direct efficient in vivo editing in mouse livers with no detectable off-target mutations. VIVO provides a general strategy for defining and quantifying the off-target effects of gene-editing nucleases in whole organisms, thereby providing a blueprint to foster the development of therapeutic strategies that use in vivo gene editing.

Immunotoxins are fusion proteins consisting of two elements, a targeting and a toxin moiety, and are designed for specific elimination of tumor cells. Previously we expressed a recombinant fusion protein consisting of the toxic fragment of Shiga toxin (A1) and GMCSF (A1-GMCSF) in Escherichia coli, and evaluated its cytotoxic properties in acute myeloid leukemia and colon carcinoma cell lines. In view of the specific cytotoxic effects of this immunotoxin, further detailed in-vitroand preclinical studies were undertaken. Large amounts of the recombinant protein of high purity and free of unwanted side products, such as lipopolysaccharides (LPS), were required. Since GMCSF is of mammalian origin and it requires proper disulfide bond formation, we intended to use the baculovirus expression vector system (BEVS) for the expression of the recombinant fusion protein. However, despite previous reports on the expression of several other immunotoxins by this system, the A1 derived fusion proteins revealed an inhibitory effect on baculoviral particle formation and even caused cell death in insect cells. This observation was further pursued and confirmed by the use of other baculoviral specific promoters. The salient features of this finding are described below.

We present a novel homogeneous in vitro assay format and apply it to the quantitative determination of the enzymatic activity of a tyrosine kinase. The assay employs a short peptidic substrate containing a single tyrosine and a single probe attached via a cysteine side chain. The structural flexibility of the peptide allows for the dynamic quenching of the probe by the nonphosphorylated tyrosine side chain. The probe responds with changes in its fluorescence lifetime depending on the phosphorylation state of the tyrosine. We use this effect to directly follow the enzymatic phosphorylation of the substrate, without having to resort to additional assay components such as an antibody against the phosphotyrosine. As an example for the application of this assay principle, we present results from the development of an assay for Abelson kinase (c-Abl) used for compound profiling. Adjustments in the peptide sequence would make this assay format suitable to a wide variety of other tyrosine kinases.

Fragment-based screening (FBS) has gained acceptance in the pharmaceutical industry as an attractive approach for the identification of new chemical starting points for drug discovery programs in addition to classical strategies such as high-throughput screening. There is the concern that screening of fragments at high µM concentrations in biochemical assays results in increased false-positive and false-negative rates. Here the authors systematically compare the data quality of FBS obtained by enzyme activity-based fluorescence intensity, fluorescence lifetime, and mobility shift assays with the data quality from surface plasmon resonance (SPR) and nuclear magnetic resonance (NMR) methods. The serine protease trypsin and the matrix metalloprotease MMP12 were selected as model systems. For both studies, 352 fragments were selected each. From the data generated, all 3 biochemical protease assay methods can be used for screening of fragments with low false-negative and low false-positive rates, comparable to those achieved with the SPR-based assays. It can also be concluded that only fragments with a solubility higher than the screening concentration determined by means of NMR should be used for FBS purposes. Extrapolated to 10,000 fragments, the biochemical assays speed up the primary FBS process by approximately a factor of 10 and reduce the protease consumption by approximately 10,000-fold compared to NMR protein observation experiments.

Fluorescence lifetime is an intrinsic parameter describing the fluorescence process. Changes in the fluorophore’s physicochemical environment can lead to changes in the fluorescence lifetime. When used as the readout in biological assays, it is thought to deliver superior results to conventional optical readouts. Hence it has the potential to replace readout technologies currently established in drug discovery such as absorption, luminescence or fluorescence intensity. Here we report the development of an activity assay for human kallikrein 7, a serine protease involved in skin diseases. As a probe, we have selected a blue-fluorescent acridone dye, featuring a remarkably long lifetime that can be quenched by either of the 2 natural amino acids, tyrosine and tryptophan. Incorporating this probe and 1 of the quenching amino acids on either side of the scissile bond of the substrate peptide enables us to monitor the enzymatic activity by quantifying the increase in the fluorescence lifetime signal. A systematic investigation of substrate structures has led to a homogenous, microplate-based, compound profiling assay that yields inhibitory constants down into the single-digit nanomolar range. This type of assay has now been added to our standard portfolio of screening techniques, and is routinely used for compound profiling.

High-throughput screening (HTS) is a well-established process in lead discovery for pharma and biotech companies and is now also being set up for basic and applied research in academia and some research hospitals. Since its first advent in the early to mid-1990s, the field of HTS has seen not only a continuous change in technology and processes but also an adaptation to various needs in lead discovery. HTS has now evolved into a quite mature discipline of modern drug discovery. Whereas in previous years, much emphasis has been put toward a steady increase in capacity (“quantitative increase”) via various strategies in the fields of automation and miniaturization, the past years have seen a steady shift toward higher content and quality (“quality increase”) for these biological test systems. Today, many experts in the field see HTS at the crossroads with the need to decide either toward further increase in throughput or more focus toward relevance of biological data. In this article, the authors describe the development of HTS over the past decade and point out their own ideas for future directions of HTS in biomedical research. They predict that the trend toward further miniaturization will slow down with the implementation of 384-well, 1536-well, and 384 low-volume-well plates. The authors predict that, ultimately, each hit-finding strategy will be much more project related, tailor-made, and better integrated into the broader drug discovery efforts.

The 10th anniversary of MipTec, which took place in Basel, Switzerland on 7 – 10 May 2007, demonstrated that this meeting has truly evolved into the leading European event for drug discovery technologies. The rich programme included sessions on drug discovery processes, structure-based drug design, pharmacodynamics and biomarkers, maximizing compound value, drug discovery technologies or emerging absorption, distribution, metabolism and excretion/toxicity technologies together with keynote presentations providing the larger picture, an excellent poster session and a well-attended vendor exhibition. In summary, MipTec more than ever provides a much needed hub for scientific exchange and networking within the European drug discovery community.

High-throughput screening of chemical libraries for compounds that interfere with a particular molecular target is among the most powerful methodologies applied in lead discovery at present. In this review, the authors describe a label-free, homogeneous, affinity-selection-based technology developed at Novartis, termed SpeedScreen, which is compared with similar technologies used for high-throughput screening in the pharmaceutical and biotechnology industries. The focus at present of SpeedScreen is twofold: first, this technology is applied to orphan genomic targets and to those targets that are non-tractable by a functional assay; second, this technology is applied complementary to the well-established traditional methodologies for the screening of molecular targets. In summary, the authors discuss the value of affinity-selection-based high-throughput screening as a complementary technology to the common functional screening platforms and the benefits as well as the limitations of this new technology are outlined.

This article discusses the development of homogeneous, miniaturized assays for the identification of novel kinase inhibitors from very large compound collections. In particular, the suitability of time-resolved fluorescence resonance energy transfer (TR-RET) based on phospho-specific antibodies, an antibody-independent fluorescence polarization (FP) approach using metal-coated beads (IMAP™ technology), and the determination of adenosine triphosphate consumption through chemiluminescence is evaluated. These readouts are compared with regard to assay sensitivity, compound interference, reagent consumption, and performance in a 1536-well format, and practical considerations for their application in primary screening or in the identification of kinase substrates are discussed. All of the tested technologies were found to be suitable for miniaturized high-throughput screening (HTS) in principle, but each of them has distinct limitations and advantages. Therefore, the target-specific selection of the most appropriate readout technology is recommended to ensure maximal relevance of HTS campaigns.

The 9th annual MipTec conference was held in Basel, Switzerland on 8 – 11 May 2006 and was preceded by a preconference including a variety of well-established speakers highlighting various aspects of the drug discovery process from a more general perspective. The main conference was thoughtfully organised into sessions on structure-based drug design, drug discovery processes, drug discovery technologies, pharmacodynamics and biomarkers, and maximising compound value. Here the authors attempt to ‘cherry pick’ some personal highlights from the many presentations in the sessions.

This article discusses the development of homogeneous, miniaturized assays for the identification of novel kinase inhibitors from very large compound collections. In particular, the suitability of time-resolved fluorescence resonance energy transfer (TR-RET) based on phospho-specific antibodies, an antibody-independent fluorescence polarization (FP) approach using metal-coated beads (IMAP™ technology), and the determination of adenosine triphosphate consumption through chemiluminescence is evaluated. These readouts are compared with regard to assay sensitivity, compound interference, reagent consumption, and performance in a 1536-well format, and practical considerations for their application in primary screening or in the identification of kinase substrates are discussed. All of the tested technologies were found to be suitable for miniaturized high-throughput screening (HTS) in principle, but each of them has distinct limitations and advantages. Therefore, the target-specific selection of the most appropriate readout technology is recommended to ensure maximal relevance of HTS campaigns.

The high-throughput affinity-selection screening platform SpeedScreen was recently reported by the Novartis Institutes for BioMedical Research as a homogeneous, label-free screening technology with mass-spectrometry readout. SpeedScreen relies on the screening of compound mixtures with various target proteins and uses fast size-exclusion chromatography to separate target-bound from unbound substances. After disintegration of the target-binder complex, the binder molecules are identified by their molecular masses using liquid chromatography/mass spectrometry. The authors report an analysis of the molecular properties of hits obtained with SpeedScreen on 26 targets screened within the past few years at Novartis using this technology. Affinity-based SpeedScreen is a robust high-throughput screening technology that does not accumulate frequent hitters or potential covalent binders. The hits are representative of the most commonly identified scaffold classes observed for known drugs. Validated SpeedScreen hits tend to be enriched on more lipophilic and larger-molecular-weight compounds compared to the whole library. The potential for a reduced SpeedScreen screening set to be used in case only limited protein quantities are available is evaluated. Such a reduced compound set should also maximize the coverage of the high-performing regions of the chemical property and class spaces; chemoinformatics methods including genetic algorithms and divisive K-means clustering are used for this aim.

The high-throughput affinity-selection screening platform SpeedScreen was recently reported by the Novartis Institutes for BioMedical Research as a homogeneous, label-free screening technology with mass-spectrometry readout. SpeedScreen relies on the screening of compound mixtures with various target proteins and uses fast size-exclusion chromatography to separate target-bound from unbound substances. After disintegration of the target-binder complex, the binder molecules are identified by their molecular masses using liquid chromatography/mass spectrometry. The authors report an analysis of the molecular properties of hits obtained with SpeedScreen on 26 targets screened within the past few years at Novartis using this technology. Affinity-based SpeedScreen is a robust high-throughput screening technology that does not accumulate frequent hitters or potential covalent binders. The hits are representative of the most commonly identified scaffold classes observed for known drugs. Validated SpeedScreen hits tend to be enriched on more lipophilic and larger-molecular-weight compounds compared to the whole library. The potential for a reduced SpeedScreen screening set to be used in case only limited protein quantities are available is evaluated. Such a reduced compound set should also maximize the coverage of the high-performing regions of the chemical property and class spaces; chemoinformatics methods including genetic algorithms and divisive K-means clustering are used for this aim.

The beta isoform of the heat shock protein 90 (Hsp90β) is a cellular chaperone required for the maturation of key proteins involved in growth response to extracellular factors as well as oncogenic transformation of various cell types. Compounds that inhibit the function of Hsp90β are thus believed to have potential as novel anticancer drugs. To date, 2 fungal metabolites are known to inhibit Hsp90β. However, insolubility and liver toxicity restrict the clinical use of these molecules. The limitation to identify novel and safe Hsp90β inhibitors is that presently no suitable high-throughput screening assay is available. Here, the authors present the development of a homogenous assay based on 2-dimensional fluorescence intensity distribution analysis of tetramethyl-rhodamine (TAMRA)-labeled radicicol bound to Hsp90β. Furthermore, the assay has been shown to be compatible with the confocal nanoscreening platform Mark II™ from Evotec-Technologies and can therefore be used for miniaturized high-throughput screening. The applied detection technology provides critical information about the nature of biomolecular interaction at the thermodynamic equilibrium, such as affinity constants and stoichiometric parameters of the binding. The assay is used to identify small molecular weight compounds displacing TAMRA-radicicol. Such compounds are believed to be important molecules in the discovery of novel anticancer drugs.

The beta isoform of the heat shock protein 90 (Hsp90β) is a cellular chaperone required for the maturation of key proteins involved in growth response to extracellular factors as well as oncogenic transformation of various cell types. Compounds that inhibit the function of Hsp90β are thus believed to have potential as novel anticancer drugs. To date, 2 fungal metabolites are known to inhibit Hsp90β. However, insolubility and liver toxicity restrict the clinical use of these molecules. The limitation to identify novel and safe Hsp90β inhibitors is that presently no suitable high-throughput screening assay is available. Here, the authors present the development of a homogenous assay based on 2-dimensional fluorescence intensity distribution analysis of tetramethyl-rhodamine (TAMRA)-labeled radicicol bound to Hsp90β. Furthermore, the assay has been shown to be compatible with the confocal nanoscreening platform Mark II™ from Evotec-Technologies and can therefore be used for miniaturized high-throughput screening. The applied detection technology provides critical information about the nature of biomolecular interaction at the thermodynamic equilibrium, such as affinity constants and stoichiometric parameters of the binding. The assay is used to identify small molecular weight compounds displacing TAMRA-radicicol. Such compounds are believed to be important molecules in the discovery of novel anticancer drugs. (Journal ofBiomolecular Screening2004:569-577)

SpeedScreen is a novel, label-free, in-solution, affinity-based selection methodology for high-throughput screening (HTS) developed at Novartis Pharma. The SpeedScreen protocol comprises in-solution affinity selection, followed by size exclusion chromatography in combination with microbore-liquid-chromatography/electrospray-ionization mass spectrometry (micro-LC/ESI-MS). The authors describe the basic concept behind assay development, HTS, and data analysis with the SpeedScreen technology. Advantages and limitations of SpeedScreen compared to alternative screening technologies are discussed, and an example is given from a SpeedScreen campaign applying this innovative affinity selection concept in HTS.

SpeedScreen is a novel, label-free, in-solution, affinity-based selection methodology for high-throughput screening (HTS) developed at Novartis Pharma. The SpeedScreen protocol comprises in-solution affinity selection, followed by size exclusion chromatography in combination with microbore-liquid-chromatography/electrospray-ionization mass spectrometry (micro-LC/ESI-MS). The authors describe the basic concept behind assay development, HTS, and data analysis with the SpeedScreen technology. Advantages and limitations of SpeedScreen compared to alternative screening technologies are discussed, and an example is given from a SpeedScreen campaign applying this innovative affinity selection concept in HTS. (Journal of Biomolecular Screening2004:498-505)

Recombinant baculoviruses derived from the Autographa californicanuclear polyhedrosis virus (AcNPV) are widely used to express heterologous genes in insect cells, but the use of the baculovirus expression vector system (BEVS) is hampered by slow and tedious procedures for the selection and separation of baculovirus-infected insect cells and for titer determination. Here we developed a new technology based on the bicistronic vector with a fusion protein of the human integral plasma membrane glycoprotein CD4 and green fluorescent protein (GFP) for concomitant expression of target proteins in insect Sf21 cells. Magnetic cell sorting (MACS) technology with anti-CD4 antibody-labeled superparamagnetic beads was used to separate the baculovirus-infected from the noninfected insect cells and therefore to increase the virus titer and to reduce process time. With the herein described use of the MACS-improved baculovirus expression plasmid MACS in baculovirus expression (pMACS-iBac-1), we have been able to select the baculovirus-infected insect cells at an early time point of the infection cycle and therefore enrich the virus titer dramatically. Furthermore, simple end point dilution and GFP fluorescence detection can be used for early and facile detection of recombinant viruses and simplified titer determinations. We show that the bicistronic pMACSiBac-1 with an additional multiple cloning site under the control of the very late promoter polyhedrin (PPH) allows for the expression of target proteins in high amounts, less workloads, and shorter timelines.

Control of neurotransmitter receptor expression and delivery to the postsynaptic membrane is of critical importance for neural signal transduction at synapses. The γ-aminobutyric acid, type A (GABAA) receptor-associated protein GABARAP was reported to have an important role for movement and sorting of GABAAreceptor molecules to the postsynaptic membrane. GABARAP not only binds to GABAAreceptor γ2-subunit but also to tubulin, gephyrin, and ULK1. We present for the first time the high resolution structure of human GABARAP determined by nuclear magnetic resonance in aqueous solution. One part of the molecule, despite being well ordered and rigid on a MHz time scale, exists in at least two different conformations that interchange with each other on a time scale slower than 25 Hz. An important feature of the solution structure is the observation that amino- and carboxyl-terminal ends of the protein directly interact with each other, which is not seen in recently reported crystal structures. The possible biological relevance of these observations for the regulation of GABARAP interactions and functions is discussed.

In wild-type ribonuclease T₁the peptide bond between Tyr38 and Pro39 is in thecisconformation. When Pro39 is replaced by an alanine thiscisconformation is retained, and a non-prolylcisTyr38–Ala39 peptide bond is generated. We employed a stopped-flow double-mixing technique to investigate the kinetics of thecis→transisomerization of this peptide bond in the unfolding and thetrans→cisisomerization in the refolding of Pro39Ala-ribonuclease T₁. In 6.0 M GdmCl (pH 1.6) and 25° the protein unfolds rapidly witha time constant of 20 ms, followed by Tyr38–Ala39cis→transisomerization. This reaction shows a time constant of 730 ms and is about 60-fold faster than the isomerization of the Tyr38–Pro39 bond in the wild type protein. Unfolded molecules with the Tyr38–Ala39 bond still in the native-likecisconformation accumulate transiently for a short time after unfolding is initiated, and they can refold very rapidly to the native state with a time constant of 290 ms (in 1.0 M GdmCl, pH 4.6, 25°C). After more than three seconds of unfolding virtually all broken molecules contain an incorrecttransTyr–Ala39 bond and refolding is decelerated approximately 1000-fold, because Tyr38–ALa39trans→cisre–isomerization is very slow and, with its time constant of 480 s, determines the overall rate of refolding. Due to the coupling of thecis–transequilibrium with protein folding it was possible to measure the kinetic parameters of the isomerization of a non-prolyl peptide bond in a protein. Previously this could not be accomplished, because thetransisomer is strongly preferred for unsubstituted peptide bonds in oligopeptides under virtually all conditions. Our data indicate that the kinetics of Tyr38–Pro39 and of Tyr38–Ala39 isomerization differ predominantly in the rate of thecis→trans,rather than of thetrans→cis,reaction. The rate of thetrans→cisreaction is, however, measured during refolding and may be influenced by the formation of ordered protein structure.

The cis conformation of the 38-39 peptide bond of ribonuclease T₁ is retained after the replacement of cis Pro39 by an alanine residue. This conformation is demonstrated by the presence of a NOESY cross-peak in the NMR spectrum between the C^α protons of Tyr38 and Ala39 in the Pro39→Ala variant. The presence of this non-prolyl cis peptide bond explains the retention of the catlytic activity, the strong decrease in stability and the changes in the folding mechanism that were observed after the Pro39→Ala mutation in ribonuclease T₁. We suggest that a cis peptide bond is retained in a protein after the substitution of a cis proline at positions, where a trans bond would destabilize the protein more strongly than a non-prolyl peptide bond in the energetically unfavourable cis conformation. Copyright 1994, 1999 Academic Press

The refolding of ribonuclease T₁ involves two major slow processes that exhibit properties of prolyl isomerization reactions. A comparison of the wild-type protein and a designed variant where the cis Ser54-Pro55 bond was replaced by a Gly54-Asn55 bond indicated that the faster of these reactions is the isomerization of Pro55. Here we report the replacement of the other cis proline of ribonuclease T₁ at position 39 by alanine. The Pro39Ala variant is similar to the wild-type protein in secondary and tertiary structure, and the enzymatic activity towards RNA and a dinucleotide substrate remains almost unchanged. The fluorescence emission of the single Trp59 is lowered by the Pro39Ala substitution, probably because Trp59 is in close contact to Pro39 in wild-type ribonuclease T₁. Unlike the substitution of cis Pro55, the Pro39Ala mutation is strongly destabilizing and reduces the Gibbs free energy of the folded protein by about 20 kJ/mol. Pro39 is buried in native RNase T₁ and located near the active site. The observed destabilization could originate from the presence of a cis alanyl bond in the Pro39Ala variant or from a local distortion caused by the incorporation of a trans alanyl peptide bond in the interior of the protein. In the refolding kinetics the replacement of Pro39 leads to a disappearance of the fast-refolding species. Refolding still involves two consecutive slow steps. The first and faster step could be the isomerization of the remaining cis Pro55. The second, very slow step is a novel reaction that appears to have no counterpart in the refolding of the wild-type protein. All mutant molecules must undergo this reaction before reaching the native state. These major changes in the folding kinetics strongly indicate that cis-Pro39 is indeed of major importance for the folding of the wild-type protein. They indicate, moreover, that some new feature of protein folding kinetics is observed in these studies of the Pro39Ala variant. Copyright 1993, 1999 Academic Press

The replacement of cis proline 39 of ribonuclease T₁ by an alanine residue leads to a decrease in stability by about 20 kJ/mol and to major changes in the folding kinetics that are not easily explained by the proline model for protein folding. In particular, a novel very slow reaction is observed in the refolding of the Pro39Ala variant. Here the unfolding and refolding kinetics of this protein are further investigated. We show that the very slow reaction is not a prolyl isomerization. It is not created by a slow isomerization of the unfolded protein, nor is it catalyzed by prolyl isomerase, and all molecules have to undergo this reaction during refolding. Most of the unfolded Pro39Ala molecules contain an incorrect trans isomer at the remaining cis Pro55. They use a sequential pathway for refolding, in which trans to cis isomerization at Pro55 precedes the very slow reaction. The refolding of the minor fraction of unfolded Pro39Ala molecules with a correct cis isomer at proline 55 is a single first-order reaction that is limited in rate by the very slow step. The folding mechanism of wild-type ribonuclease T₁ cannot be used to explain these results and independent mechanisms are proposed to model the unfolding and refolding of the Pro39Ala variant. The molecular interpretation of the changes in the folding mechanism is tied to the question, as to whether the cis character of the peptide bond at position 38-39 is maintained after the substitution of Pro39 by alanine. A possible explanation could be that the novel very slow folding reaction involves the trans to cis isomerization of the Tyr38-Ala39 bond. Such a reaction is probably slow, since the activation energy is high and since tight coupling with the formation of structure is required to stabilize the cis form of a non-prolyl peptide bond. Alternatively, the strong decrease in folding rate could be correlated with the general destabilization of ribonuclease T₁ by the Pro39Ala mutation. Copyright 1993, 1999 Academic Press