OBJECTIVE:Nutrient-stimulated gut hormone peptide YY3-36 (PYY3-36) selectively activates the neuropeptide Y2 receptor (NPY2R) and reduces energy intake in humans. We describe the discovery and pharmacology of the long-acting NPY2R agonist BI 1820237 and its potential bodyweight-lowering efficacy alone and in combination with the glucagon receptor (GCGR)/glucagon-like peptide-1 receptor (GLP-1R) dual agonist survodutide. METHODS & RESULTS:BI 1820237 dose-dependently reduced food intake and gastric emptying in lean mice. Significant bodyweight reductions were not observed with BI 1820237 alone in diet-induced obese mice, however combination with survodutide led to bodyweight reduction of 22% which was significantly (p < 0.01) greater than the 17% bodyweight reduction with survodutide alone. Regression-based interaction analysis demonstrated that BI 1820237 increased the efficacy of survodutide by 265% at an ED50 of 11.7 nmol/kg over a range of dose combinations. CONCLUSION:Synergistic NPY2R and GCGR/GLP-1R agonism provides an attractive mode of action for clinically relevant weight loss in patients with obesity.

Objective: Obesity is a major global health problem which can be targeted with new mechanistic diverse pharmacological interventions. Here we evaluate a new long-acting secretin receptor agonist as a potential treatment for obesity. Methods: BI-3434 was designed as a secretin analog with stabilized peptide backbone and attached fatty acid-based half-life extension group. The peptide was evaluated in vitro for its ability to stimulate cAMP accumulation in a cell line stably expressing recombinant secretin receptor. On the functional level, stimulation of lipolysis in primary adipocytes after treatment with BI-3434 was determined. The ability of BI-3434 to activate secretin receptor in vivo was assessed in a cAMP reporter CRE-Luc mouse model. Furthermore, a diet-induced obesity mouse model was used to test the effects of BI-3434 on body weight and food intake following repeated daily subcutaneous administration alone and in combination with a GLP-1R agonist. Results: BI-3434 potently activated human secretin receptor. However, lipolysis was only weakly induced in primary murine adipocytes. BI-3434 had an extended half-life compared to endogenous secretin and activated target tissues like pancreas, adipose tissue, and stomach in vivo. BI3434 did not lower food intake in lean or diet-induced obese mice, but it increased energy expenditure after daily administration. This led to a loss of fat mass, which did not translate in a significant effect on body weight. However, treatment in combination with a GLP-1R agonist led to a synergistic effect on body weight loss. Conclusions: BI-3434 is a highly potent and selective agonist of secretin receptor with an extended pharmacokinetic (PK) profile. Increased energy expenditure after daily treatment with BI-3434 suggests that secretin receptor is involved in metabolic regulation and energy homeostasis. Targeting secretin receptor alone may not be an efficient anti-obesity treatment, but could be combined with anorectic principles like GLP-1R agonists. (c) 2023 Boehringer Ingelheim Pharma GmbH&Co.KG. Published by Elsevier GmbH.

We present an easy, human-readable line notation to describe even complex peptides.

OBJECTIVE:Obesity and its associated comorbidities represent a global health challenge with a need for well-tolerated, effective, and mechanistically diverse pharmaceutical interventions. Oxyntomodulin is a gut peptide that activates the glucagon receptor (GCGR) and glucagon-like peptide-1 receptor (GLP-1R) and reduces bodyweight by increasing energy expenditure and reducing energy intake in humans. Here we describe the pharmacological profile of the novel glucagon receptor (GCGR)/GLP-1 receptor (GLP-1R) dual agonist BI 456906. METHODS:BI 456906 was characterized using cell-based in vitro assays to determine functional agonism. In vivo pharmacological studies were performed using acute and subchronic dosing regimens to demonstrate target engagement for the GCGR and GLP-1R, and weight lowering efficacy. RESULTS:BI 456906 is a potent, acylated peptide containing a C18 fatty acid as a half-life extending principle to support once-weekly dosing in humans. Pharmacological doses of BI 456906 provided greater bodyweight reductions in mice compared with maximally effective doses of the GLP-1R agonist semaglutide. BI 456906's superior efficacy is the consequence of increased energy expenditure and reduced food intake. Engagement of both receptors in vivo was demonstrated via glucose tolerance, food intake, and gastric emptying tests for the GLP-1R, and liver nicotinamide N-methyltransferase mRNA expression and circulating biomarkers (amino acids, fibroblast growth factor-21) for the GCGR. The dual activity of BI 456906 at the GLP-1R and GCGR was supported using GLP-1R knockout and transgenic reporter mice, and an ex vivo bioactivity assay. CONCLUSIONS:BI 456906 is a potent GCGR/GLP-1R dual agonist with robust anti-obesity efficacy achieved by increasing energy expenditure and decreasing food intake.

BI 4569 is a synthetic peptide optimized to simultaneously engage the GCGR and GLP-1R. BI 4569 contains a fatty acid-based half-life extension that supports once-weekly subcutaneous injection in humans, and is currently in clinical investigation in patients with obesity or NASH. BI 4569 activates the human GCGR and GLP-1R in 100% human plasma with a potency (EC50) of 6.3 nM and 1 nM, respectively. BI 4569 potently increases glucose-stimulated insulin secretion from mouse islets (EC50 5.7 nM) and insulin secretion from perifused human islets. On single injection in lean mice, BI 4569 dose-dependently reduced food intake (FI) , gastric emptying (GE) and improved oral glucose tolerance (oGTT) with an ED50 of 90, 41, and 2.1 nmol/kg, respectively. Based on dose-dependent changes in liver NNMT mRNA and plasma amino acids, BI 4569 engages the GCGR, unlike semaglutide. Receptor-specificity of target engagement was further shown in GLP-1R knockout mice (FI, GE, oGTT) . The bodyweight-lowering efficacy of BI 4569 (3, 10, 20, 30 nmol/kg) was compared with semaglutide (20, 100 nmol/kg) in diet-induced obese mice. After 4 weeks of daily dosing, BI 4569 showed a superior bodyweight-lowering efficacy (32% at 30 nmol/kg, p≤0.0vs. vehicle) compared with a maximally effective dose of semaglutide (27% at 100 nmol/kg; p≤0.0vs. vehicle) . This greater bodyweight-lowering efficacy of BI 4569 was associated with changes in GCGR target engagement biomarkers, such as liver lipids, NNMT mRNA, plasma glucagon, FGF21, and cholesterol. Mechanistically, the superior bodyweight-lowering efficacy of BI 4569 was attributed to an increase in energy expenditure (measured at and 20 nmol/kg) . In summary, the preclinical characterization of the novel dual GCGR/GLP-1R agonist BI 4569 provides strong evidence for its clinical benefit in patients with obesity and associated comorbidities. Disclosure T. Zimmermann: Employee; Boehringer Ingelheim Pharma GmbH&Co.KG. L. Thomas: Employee; Boehringer Ingelheim International GmbH. T. Baader-Pagler: Employee; Boehringer Ingelheim International GmbH. P. Haebel: Employee; Boehringer Ingelheim International GmbH. H. Neubauer: Employee; Boehringer Ingelheim International GmbH. E. Simon: Employee; Boehringer Ingelheim Pharma GmbH&Co KG. W. Reindl: Employee; Boehringer Ingelheim International GmbH. B. Bajrami: None. W. Rist: Employee; Boehringer Ingelheim International GmbH. I. Uphues: Employee; Boehringer Ingelheim International GmbH. R. Augustin: None.

Dipeptidyl peptidase IV (DPP-IV) inhibitors improve glycemic control by prolonging the action of glucagon-like peptide-1 (GLP-1). In contrast to GLP-1 analogues, DPP-IV inhibitors are weight-neutral. DPP-IV cleavage of PYY and NPY gives rise to PYY3-36 and NPY3-36 which exert potent anorectic action by stimulating Y2 receptor (Y2R) function. This invites the possibility that DPP-IV inhibitors could be weight-neutral by preventing conversion of PYY/NPY to Y2R-selective peptide agonists. We therefore investigated whether co-administration of an Y2R-selective agonist could unmask potential weight lowering effects of the DDP-IV inhibitor linagliptin. Male diet-induced obese (DIO) mice received once daily subcutaneous treatment with linagliptin (3 mg/kg), a Y2R-selective PYY3-36 analogue (3 or 30 nmol/kg) or combination therapy for 14 days. While linagliptin promoted marginal weight loss without influencing food intake, the PYY3-36 analogue induced significant weight loss and transient suppression of food intake. Both compounds significantly improved oral glucose tolerance. Because combination treatment did not further improve weight loss and glucose tolerance in DIO mice, this suggests that potential negative modulatory effects of DPP-IV inhibitors on endogenous Y2R peptide agonist activity is likely insufficient to influence weight homeostasis. Weight-neutrality of DPP-IV inhibitors may therefore not be explained by counter-regulatory effects on PYY/NPY responses.

Chapter 13 APPLICATIONS OF CHEMINFORMATICS IN PHARMACEUTICAL RESEARCH EXPERIENCES AT BOEHRINGER INGELHEIM IN GERMANY Bernd Beck, Bernd BeckSearch for more papers by this authorMichael Bieler, Michael BielerSearch for more papers by this authorPeter Haebel, Peter HaebelSearch for more papers by this authorAndreas Teckentrup, Andreas TeckentrupSearch for more papers by this authorAlexander Weber, Alexander WeberSearch for more papers by this authorNils Weskamp, Nils WeskampSearch for more papers by this author Bernd Beck, Bernd BeckSearch for more papers by this authorMichael Bieler, Michael BielerSearch for more papers by this authorPeter Haebel, Peter HaebelSearch for more papers by this authorAndreas Teckentrup, Andreas TeckentrupSearch for more papers by this authorAlexander Weber, Alexander WeberSearch for more papers by this authorNils Weskamp, Nils WeskampSearch for more papers by this author Book Editor(s):Jürgen Bajorath, Jürgen BajorathSearch for more papers by this author First published: 21 October 2013 https://doi.org/10.1002/9781118742785.ch13 AboutPDFPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShareShare a linkShare onFacebookTwitterLinked InRedditWechat Summary CI as a discipline can look back over a 10+ year's history at BI in Germany. Aim of this chapter is to give a short overview over a number of important CI tools and systems that have been established over this period and that form the basis of our daily work. Subsequently, we show a number of typical work packages and different application examples for CI methods. Our intention is to show the broad range of topics and questions to which CI as a discipline can contribute in an industrial environment, to highlight obstacles, success factors and to point out future areas of development. Chemoinformatics for Drug Discovery RelatedInformation

We introduce the SAR matrix data structure that is designed to elucidate SAR patterns produced by groups of structurally related active compounds, which are extracted from large data sets. SAR matrices are systematically generated and sorted on the basis of SAR information content. Matrix generation is computationally efficient and enables processing of large compound sets. The matrix format is reminiscent of SAR tables, and SAR patterns revealed by different categories of matrices are easily interpretable. The structural organization underlying matrix formation is more flexible than standard R-group decomposition schemes. Hence, the resulting matrices capture SAR information in a comprehensive manner.

Baculoviruses are ubiquitous insect viruses well known for their use as bioinsecticides, gene therapy vectors, and protein expression systems. Overexpression of recombinant proteins in insect cell culture utilizes the strong promoter of the polyhedrin gene. In infected larvae, the polyhedrin protein forms robust intracellular crystals called polyhedra, which protect encased virions for prolonged periods in the environment. Polyhedra are produced by two unrelated families of insect viruses, baculoviruses and cypoviruses. The atomic structure of cypovirus polyhedra revealed an intricate packing of trimers, which are interconnected by a projecting N-terminal helical arm of the polyhedrin molecule. Baculovirus and cypovirus polyhedra share nearly identical lattices, and the N-terminal region of the otherwise unrelated baculovirus polyhedrin protein sequence is also predicted to be α-helical. These results suggest homology between the proteins and a common structural basis for viral polyhedra. Here, we present the 2.2-Å structure of baculovirus polyhedra determined by x-ray crystallography from microcrystals produced in vivo. We show that the underlying molecular organization is, in fact, very different. Although both polyhedra have nearly identical unit cell dimensions and share I23 symmetry, the polyhedrin molecules are structurally unrelated and pack differently in the crystals. In particular, disulfide bonds and domain-swapped N-terminal domains stabilize the building blocks of baculovirus polyhedra and interlocking C-terminal arms join unit cells together. We show that the N-terminal projecting helical arms have different structural roles in baculovirus and cypovirus polyhedra and conclude that there is no structural evidence for a common evolutionary origin for both classes of polyhedra.

The development of farnesyltransferase inhibitors directed against Plasmodium falciparum is a strategy towards new drugs against malaria. Previously, we described benzophenone-based farnesyltransferase inhibitors with high in vitro antimalarial activity but no in vivo activity. Through the introduction of a methylpiperazinyl moiety, farnesyltransferase inhibitors with in vivo antimalarial activity were obtained. Subsequently, a structure-based design approach was chosen to further improve the antimalarial activity of this type of inhibitor. As no crystal structure of the farnesyltransferase of the target organism is available, homology modeling was used to reveal differences between the active sites of the rat/human and the P. falciparum farnesyltransferase. Based on flexible docking data, the piperazinyl moiety was replaced by a N,N,N'-trimethylethylenediamine moiety. This resulted in an inhibitor with significantly improved in vitro and in vivo antimalarial activity. Furthermore, this inhibitor displayed a notable increase in selectivity towards malaria parasites relative to human cells.

Tough cubes Insect viruses that produce infectious polyhedra — crystals encapsulating thousands of virus particles — are widespread and important. The polyhedra microcrystals are remarkably stable, which can cause disease persistence, threatening silkworm cocoon harvests for instance. The molecular structure of one of these crystals has now been determined. This is a major technical feat in protein X-ray microcrystallography, as these viruses are the smallest protein crystals ever used to determine atomic structure. The study reveals robust polyhedra that could be useful as delivery capsules for biopesticides and for nanobiotechnology applications such as microarrays.

The crystal structure of the catalytic fragment of a Sulfolobus solfataricus P-type ATPase, CopB-B, was determined with a 2.6 A resolution. CopB-B is the major soluble fragment of the archaeal CPx-ATPase CopB and is comprized of a nucleotide and a phosphorylation domain. In the crystalline state two molecules of CopB-B are in close contact to each other, although the presence of dimers in free solution could be ruled out by analytical ultracentrifugation. The overall architecture of CopB-B is similar to that of other P-type ATPases such as Ca-ATPase. Short peptide segments are linking the nucleotide binding to the phosphorylation domain. CopB-B exhibits 33% sequence identity (of 216 aligned residues) with the respective fragment of the Archaeoglobus fulgidus ATPase CopA. The CopB-B nucleotide-binding domain has the most primitive fold yet identified for this enzyme class. It is 24% identical to the nucleotide-binding domain of the disease-related Wilson ATPase ATP7B (80 structurally aligned residues). Structural superposition with Ca-ATPase suggests a putative nucleotide-binding site in CopB-B. The phosphorylation domain of CopB-B is structurally related to the corresponding part of Ca-ATPase in the anion-bound E2 state. In CopB-B crystals, a bound sulfate anion was identified at the phosphate-binding location. In solution state, the potential binding of CopB-B to phosphate was probed with (32)P(i). Bound phosphate could be readily displaced by orthovanadate at submillimolar concentration as well as by sulfate at millimolar concentration. It is possible therefore to assign the structure of the sulfate-bound phosphorylation domain of CopB-B to a state related to the E2.P(i) intermediate state of the catalytic cycle.

The enzyme S-adenosylmethionine:tRNA ribosyltransferase-isomerase (QueA) is involved in the biosynthesis of the hypermodified tRNA nucleoside queuosine. It is unprecedented in nature as it uses the cofactor S-adenosylmethionine as the donor of a ribosyl group. We have determined the crystal structure of Bacillus subtilis QueA at a resolution of 2.9A. The structure reveals two domains representing a 6-stranded beta-barrel and an alpha beta alpha-sandwich, respectively. All amino acid residues invariant in the QueA enzymes of known sequence cluster at the interface of the two domains indicating the localization of the substrate binding region and active center. Comparison of the B. subtilis QueA structure with the structure of QueA from Thermotoga maritima suggests a high domain flexibility of this enzyme.

Less toxic drugs are needed to combat the human parasite Trypanosoma cruzi (Chagas's disease). One novel target for antitrypanosomal drug design is farnesyltransferase. Several farnesyltransferase inhibitors based on the benzophenone scaffold were assayed in vitro and in vivo with the parasite. The common structural feature of all inhibitors is an amino function which can be protonated. Best in vitro activity (LC50 values 1 and 10 nM, respectively) was recorded for the R-phenylalanine derivative 4a and for the N-propylpiperazinyl derivative 2f. These inhibitors showed no cytotoxicity to cells. When tested in vivo, the survival rates of infected animals receiving the inhibitors at 7 mg/kg body weight/day were 80 and 60% at day 115 postinfection, respectively.