Suppression of premature termination codons (PTCs) by translational readthrough is a promising strategy to treat a wide variety of severe genetic diseases caused by nonsense mutations. Here, we present two potent readthrough promoters-NVS1.1 and NVS2.1-that restore substantial levels of functional full-length CFTR and IDUA proteins in disease models for cystic fibrosis and Hurler syndrome, respectively. In contrast to other readthrough promoters that affect stop codon decoding, the NVS compounds stimulate PTC suppression by triggering rapid proteasomal degradation of the translation termination factor eRF1. Our results show that this occurs by trapping eRF1 in the terminating ribosome, causing ribosome stalls and subsequent ribosome collisions, and activating a branch of the ribosome-associated quality control network, which involves the translational stress sensor GCN1 and the catalytic activity of the E3 ubiquitin ligases RNF14 and RNF25.

With increasing protein therapeutics being designed as non-mAb (non-monoclonal antibody) modalities, additional efforts and resources are required to develop and characterize such therapeutic proteins. Truncation is an emerging issue for manufacturing of non-mAb drug substances and requires sophisticated methods to investigate. In this paper, we describe two cases with complex truncation problems where traditional methods such as intact mass spectrometry led to inclusive or wrong identifications. Therefore, we developed an online top-down LC-MS (liquid chromatography-mass spectrometry) based workflow to study truncated drug substances, and we successfully identified the clipping locations. Compared to other orthogonal methods, this method provides a unique capability of solving protein clipping problems. The successful identification of truncated species and the high compatibility to routine intact MS make it a very valuable tool for resolving truncation problems during protein production in the pharmaceutical industry.

Mass spectrometry (MS) is increasingly present in all stages of therapeutic protein discovery and development. The volume of produced data is consequently high and interpretation and reporting of analytical results is highly time and labor consuming. Key information must be extracted from these data and reported to assess critical quality attributes (CQA) which will eventually enable discovery, selection and developability assessment of therapeutic protein drug candidates. We have developed an IT environment and a series of workflows using Genedata Expressionist to automatically process, interpret and report protein mass spectrometry data generated on different MS platforms located in various locations of our research organization. Our approach enabled reduction of data volume and CPU-intense processing and allowed for 24/7 processing of data. CQAs such as identity, integrity, and PTM modifications are determined and automatically reported using template reports We will present strategies for bispecific antibody MS characterization and provide a set of examples describing automated determination of molecular mass and assessment of chain pairing.

A diverse range of selective FGFR4 inhibitor hit series were identified using unbiased screening approaches and by the modification of known kinase inhibitor scaffolds. In each case the origin of the selectivity was consistent with an interaction with a poorly conserved cysteine residue within the middle-hinge region of the kinase domain of FGFR4, at position 552. Targeting this region identified a non-covalent diaminopyrimidine series differentiating by size, an irreversible-covalent inhibitor in which Cys552 undergoes an SNAr reaction with a 2-chloropyridine, and a reversible-covalent inhibitor series in which Cys552 forms a hemithioacetal adduct with a 2-formyl naphthalene. In addition, the introduction of an acrylamide into a known FGFR scaffold identified a pan-FGFR inhibitor which reacted with both Cys552 and a second poorly conserved cysteine on the P-loop of FGFR4 at position 477 which is present in all four FGFR family members.

GPR15 is an orphan G protein-coupled receptor (GPCR) that is found in lymphocytes. It functions as a co-receptor of simian immunodeficiency virus and HIV-2 and plays a role in the trafficking of T cells to the lamina propria in the colon and to the skin. We describe the purification from porcine colonic tissue extracts of an agonistic ligand for GPR15 and its functional characterization. In humans, this ligand, which we named GPR15L, is encoded by the gene C10ORF99 and has some features similar to the CC family of chemokines. GPR15L was found in some human and mouse epithelia exposed to the environment, such as the colon and skin. In humans, GPR15L was also abundant in the cervix. In skin, GPR15L was readily detected after immunologic challenge and in human disease, for example, in psoriatic lesions. Allotransplantation of skin from Gpr15l-deficient mice onto wild-type mice resulted in substantial graft protection, suggesting nonredundant roles for GPR15 and GPR15L in the generation of effector T cell responses. Together, these data identify a receptor-ligand pair that is required for immune homeostasis at epithelia and whose modulation may represent an alternative approach to treating conditions affecting the skin such as psoriasis.

Bisphosphonates are potent inhibitors of farnesyl pyrophosphate synthase (FPPS) and are highly efficacious in the treatment of bone diseases such as osteoporosis, Paget's disease and tumor-induced osteolysis. In addition, the potential for direct antitumor effects has been postulated on the basis of in vitro and in vivo studies and has recently been demonstrated clinically in early breast cancer patients treated with the potent bisphosphonate zoledronic acid. However, the high affinity of bisphosphonates for bone mineral seems suboptimal for the direct treatment of soft-tissue tumors. Here we report the discovery of the first potent non-bisphosphonate FPPS inhibitors. These new inhibitors bind to a previously unknown allosteric site on FPPS, which was identified by fragment-based approaches using NMR and X-ray crystallography. This allosteric and druggable pocket allows the development of a new generation of FPPS inhibitors that are optimized for direct antitumor effects in soft tissue.

Therapeutic antibody assessment in biofluids requires fit-for-purpose bioanalytical methods. The reference is the immunoassay, the accuracy of which may be compromised by interference by endogenous components. Here, we report the inherent analytical problems posed by immunoassays and propose an alternative based on LC-MS that should be readily applicable to the analysis of therapeutic antibodies in biological fluids. We review problems linked to assay sensitivity, the choice of the assay format involving either immunodetection or MS, and strategies in the assessment of bound versus free forms.

Therapeutic antibody assessment in biofluids requires fit-for-purpose bioanalytical methods. The reference is the immunoassay, the accuracy of which may be compromised by interference by endogenous components. Here we report the inherent analytical problems posed by immunoassays and propose an alternative based on liquid chromatography/mass spectrometry that should be readily applicable to analysis of therapeutic antibodies in biological fluids. We review problems linked to assay sensitivity, the choice of the assay format involving either immunodetection or mass spectrometry, and strategies in the assessment of bound vs. free forms.

The development of a quantification method for monoclonal antibodies in serum has been accomplished by high-performance liquid chromatography multiple reactions monitoring mass spectrometry. A human monoclonal antibody (HmAb) was used as the model protein for method development and validation. A peptide from the CDR3-region of its heavy chain was selected and used for quantifying the entire mAb. This signature peptide served as a template for the internal standard. Prior to mass spectrometric analysis approximately 50% of the total serum protein content was removed by albumin depletion. The accuracy of the method ranged between 99 and 112% in cynomolgus monkey serum. The intra-assay coefficient of variation (CV) was lower than 4% at 4 microg/mL and 200 microg/mL HmAb (n = 3). The CV at 400 microg/mL corresponded to 9% (n = 3). In addition, the interassay variation was investigated in a male cynomolgus serum pool and in a female cynomolgus serum pool. The CV for the male cynomolgus pool at 4 microg/mL HmAb was 7% (n = 3). The CV obtained from the female pool was 8% (n = 3), at 4 microg/mL. The dynamic range of the method was 3 orders of magnitude. After albumin depletion of 25 microL of serum, a lowest limit of quantification of 2 microg/mL HmAb was reached in both human and cynomolgus monkey samples.

A series of beta-lactam derivatives has been designed and synthesized to inhibit the chymotrypsin-like activity of the human 20S proteasome. The most potent compounds of this new structural class of beta-subunit selective 20S proteasome inhibitors exhibit IC50 values in the low-nanomolar range and show good selectivity over the trypsin-like and post-glutamyl-peptide hydrolytic activities of the enzyme.

24 European Crystallographic Meeting, ECM24, Marrakech, 2007 Page s119 Acta Cryst. (2007). A63, s119 MS03 P01 Three Structural Snapshots Of The FPPS Catalytic Cycle Revealed By X-Ray Analyses Jean-Michel Rondeau, Francis Bitsch, Emmanuelle Bourgier, Martin Geiser, René Hemmig, Markus Kroemer, Sylvie Lehmann, Paul Ramage, Sébastien Rieffel, André Strauss, Jonathan R. Green and Wolfgang Jahnke, Discovery Technologies and Musculoskeletal Diseases, Novartis Institutes for Biomedical Research, CH-4002, Basel, Switzerland. E-mail: jeanmichel.rondeau@novartis.com

Increasing evidence is accumulating that zoledronic acid (ZOL), a nitrogen-containing bisphosphonate (N-BP), is able to affect tumor cells by inhibiting the enzyme farnesyl pyrophosphate synthase (FPPS) in the mevalonate pathway (MVP). The consequent accumulation of unprenylated proteins is believed to largely account for the cytotoxic effects of ZOL. FPPS inhibition leads also to the accumulation of isopentenyl pyrophosphate (IPP) and the apoptotic ATP analog, ApppI, but the role of this mechanism in the cytotoxic action of bisphosphonates is less clear. Since treatment with MVP intermediates has been shown to overcome N-BP-induced apoptosis via rescuing protein prenylation, our aim here was to determine their mechanism of action on ZOL-induced IPP/ApppI accumulation.Interestingly, the results revealed that ZOL-induced IPP/ApppI accumulation in MCF-7 cells were decreased by farnesol, and almost completely blocked by geranylgeraniol and geranylpyrophosphate. The functionality of the regulatory enzymes of IPP and ApppI, IPP isomerase and aminoacyl-tRNA-synthase, respectively, or protein levels of FPPS were not affected by the treatments. However, the protein levels of 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGR) and unprenylated Rap1A were observed to be strongly downregulated by geranylgeraniol and geranylpyrophosphate.This study represents a novel insight into the mechanism of action of MVP intermediates on the regulation of MVP after FPPS inhibition. The data implies that in addition to the previously reported effects on rescuing protein prenylation, MVP intermediates can preserve cell activity by inhibiting the accumulation of IPP/ApppI via HMGR downregulation. This supports the hypothesis that IPP/ApppI formation is a significant mechanism in the anticancer action of ZOL.

To understand the structural basis for bisphosphonate therapy of bone diseases, we solved the crystal structures of human farnesyl pyrophosphate synthase (FPPS) in its unliganded state, in complex with the nitrogen-containing bisphosphonate (N-BP) drugs zoledronate, pamidronate, alendronate, and ibandronate, and in the ternary complex with zoledronate and the substrate isopentenyl pyrophosphate (IPP). By revealing three structural snapshots of the enzyme catalytic cycle, each associated with a distinct conformational state, and details about the interactions with N-BPs, these structures provide a novel understanding of the mechanism of FPPS catalysis and inhibition. In particular, the accumulating substrate, IPP, was found to bind to and stabilize the FPPS-N-BP complexes rather than to compete with and displace the N-BP inhibitor. Stabilization of the FPPS-N-BP complex through IPP binding is supported by differential scanning calorimetry analyses of a set of representative N-BPs. Among other factors such as high binding affinity for bone mineral, this particular mode of FPPS inhibition contributes to the exceptional in vivo efficacy of N-BP drugs. Moreover, our data form the basis for structure-guided design of optimized N-BPs with improved pharmacological properties.

structural enzymology, drug mechanism, activity and mechanism of enzymes Farnesyl diphosphate synthase (FPPS) is now well established as the molecular target of nitrogen-containing bisphosphonate (N-BP) drugs [1-3].We have determined the X-ray structures of human FPPS in its unliganded state, in complex with the N-BP drug zoledronic acid, and in the ternary complex with zoledronic acid and the substrate isopentenyl diphosphate (IPP).By revealing three structural snapshots of the enzyme catalytic cycle, each associated with a distinct conformational state, these structures provide a novel understanding of the mechanism of FPPS catalysis and inhibition.In particular, the accumulating substrate, IPP, was found to bind to and stabilize the FPPS/N-BP complex, rather than competing with and displacing the N-BP inhibitor.Among other factors such as efficient bone targeting, this particular mode of FPPS inhibition contributes to the exceptional in vivo efficacy of N-BP drugs.