Structure-based design of a Cortistatin analogue with immunomodulatory activity in models of inflammatory bowel disease

Ulcerative colitis and Crohn’s disease are forms of inflammatory bowel disease whose incidence and prevalence are increasing worldwide. These diseases lead to chronic inflammation of the gastrointestinal tract as a result of an abnormal response of the immune system. Recent studies positioned Cortistatin, which shows low stability in plasma, as a candidate for IBD treatment. Here, using NMR structural information, we design five Cortistatin analogues adopting selected native Cortistatin conformations in solution. One of them, A5, preserves the anti-inflammatory and immunomodulatory activities of Cortistatin in vitro and in mouse models of the disease. Additionally, A5 displays an increased half-life in serum and a unique receptor binding profile, thereby overcoming the limitations of the native Cortistatin as a therapeutic agent. This study provides an efficient approach to the rational design of Cortistatin analogues and opens up new possibilities for the treatment of patients that fail to respond to other therapies.A.Rol was a recipient of a PhD fellowship from the Generalitat de Catalunya (FI) and A.E. and E.P. were recipients of PhD fellowships granted by the Severo Ochoa Program(FPI). T.T. was a postdoctoral fellow co-funded by the Marie Skłodowska-CurieCOFUND actions (IRB Barcelona Interdisciplinary Postdoc Programme). This work wassupported by the following grants: CTQ2014-56361-P and CTQ2017-87840-P (A.Riera)and RTI2018-100700-B-100 (M.D.) from the Spanish Ministry of Economy, Industryand Competitiveness (MINECO); and by AGAUR (SGR-50). We also acknowledge institutional funding from MINECO through the Centers of Excellence Severo OchoaAward given to IRB Barcelona, as well as from the CERCA Program of the Generalitat deCatalunya. M.J.M. is an ICREA Programme Investigator

Insights into Structure-Activity Relationships of Somatostatin Analogs Containing Mesitylalanine.

The non-natural amino acid mesitylalanine (2,4,6-trimethyl-L-phenylalanine; Msa) has an electron-richer and a more conformationally restricted side-chain than that of its natural phenylalanine counterpart. Taking these properties into account, we have synthesized ten somatostatin analogs containing Msa residues in different key positions to modify the intrinsic conformational flexibility of the natural hormone. We have measured the binding affinity of these analogs and correlated it with the main conformations they populate in solution. NMR and computational analysis revealed that analogs containing one Msa residue were conformationally more restricted than somatostatin under similar experimental conditions. Furthermore, we were able to characterize the presence of a hairpin at the pharmacophore region and a non-covalent interaction between aromatic residues 6 and 11. In all cases, the inclusion of a D-Trp in the eighth position further stabilized the main conformation. Some of these peptides bound selectively to one or two somatostatin receptors with similar or even higher affinity than the natural hormone. However, we also found that multiple incorporations of Msa residues increased the life span of the peptides in serum but with a loss of conformational rigidity and binding affinity

Structure-based design of a Cortistatin analogue with immunomodulatory activity in models of inflammatory bowel disease

Ulcerative colitis and Crohn's disease are forms of inflammatory bowel disease whose incidence and prevalence are increasing worldwide. These diseases lead to chronic inflammation of the gastrointestinal tract as a result of an abnormal response of the immune system. Recent studies positioned Cortistatin, which shows low stability in plasma, as a candidate for IBD treatment. Here, using NMR structural information, we design five Cortistatin analogs adopting selected native Cortistatin conformations in soln. One of them, A5, preserves the anti-inflammatory and immunomodulatory activities of Cortistatin in vitro and in mouse models of the disease. Addnl., A5 displays an increased half-life in serum and a unique receptor binding profile, thereby overcoming the limitations of the native Cortistatin as a therapeutic agent. This study provides an efficient approach to the rational design of Cortistatin analogs and opens up new possibilities for the treatment of patients that fail to respond to other therapies

Peptide aromatic interactions modulated by fluorinated residues: Synthesis, structure and biological activity of Somatostatin analogs containing 3-(3',5'difluorophenyl)-alanine

Somatostatin is a 14-residue peptide hormone that regulates the endocrine system by binding to five G-protein-coupled receptors (SSTR1-5). We have designed six new Somatostatin analogs with L-3-(3',5'-difluorophenyl)-alanine (Dfp) as a substitute of Phe and studied the effect of an electron-poor arom. ring in the network of arom. interactions present in Somatostatin. Replacement of each of the Phe residues (positions 6, 7 and 11) by Dfp and use of a D-Trp8 yielded peptides whose main conformations could be characterized in aq. soln. by NMR. Receptor binding studies revealed that the analog with Dfp at position 7 displayed a remarkable affinity to SSTR2 and SSTR3. Analogs with Dfp at positions 6 or 11 displayed a π-π interaction with the Phe present at 11 or 6, resp. Interestingly, these analogs, particularly [D-Trp8,L-Dfp11]-SRIF, showed high selectivity towards SSTR2, with a higher value than that of Octreotide and a similar one to that of native Somatostatin

Characterization of p38α autophosphorylation inhibitors that target the non-canonical activation pathway

16 pages, 10 figures, supplementary information https://doi.org/10.1038/s41467-023-39051-x.-- Data availability: The diffraction data and coordinates of the p38α complexes bound to NC-p38i compounds have been deposited in the Protein Data Bank under accession codes 7PVU, 7Z6I and 7Z9T. We have also used the following PDB structures: 4LOO, 1A9U, 3COI, 7N8T, 2ZOQ, 1PME, 3GC9, 1CM8, 4UX9. Source data are provided with this paperp38α is a versatile protein kinase that can control numerous processes and plays important roles in the cellular responses to stress. Dysregulation of p38α signaling has been linked to several diseases including inflammation, immune disorders and cancer, suggesting that targeting p38α could be therapeutically beneficial. Over the last two decades, numerous p38α inhibitors have been developed, which showed promising effects in pre-clinical studies but results from clinical trials have been disappointing, fueling the interest in the generation of alternative mechanisms of p38α modulation. Here, we report the in silico identification of compounds that we refer to as non-canonical p38α inhibitors (NC-p38i). By combining biochemical and structural analyses, we show that NC-p38i efficiently inhibit p38α autophosphorylation but weakly affect the activity of the canonical pathway. Our results demonstrate how the structural plasticity of p38α can be leveraged to develop therapeutic opportunities targeting a subset of the functions regulated by this pathwayThis work was supported by grants from the Spanish Ministerio de Ciencia e Innovación (MICINN, PID2019-109521RB-I00 and PID2021-122478NB-I00), the BioMedTec program of IRB-Fundació La Caixa, the European Research Council (Proof of Concept p38_InTh-825763), AGAUR (2016 LLAV 00043 and 2019 PROD 00138 supported by FEDER, and 2017 SGR-557, 2017 SGR-50, 2021 SGR-909, and 2021 SGR-866), BBVA Foundation, and the European Union’s Horizon 2020 research and innovation program (euCanSHare 825903 and BioExcel-3 101093290). L.G. and B.B. were funded by predoctoral contracts from MICINN (BES-2016-077122) and the Marie Skłodowska-Curie COFUND action of IRB Barcelona and the PREBIST Predoc Programme (PREBIST_754558), respectively. F.C. is a Ramon y Cajal Fellow (RYC2019-026768-I). Access to ALBA was granted through the BAG proposals 2018092972 and 2020094472. We gratefully acknowledge institutional funding from IRB Barcelona, the CERCA Programme of the Catalan Government, and the MICINN through the Centres of Excellence Severo Ochoa award. M.J.M. and A.R.N. are supported by the Institució Catalana de Recerca i Estudis Avancats (ICREA)With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)Peer reviewe

AI is a viable alternative to high throughput screening: a 318-target study

: High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery

HTSDSF Explorer, A Novel Tool to Analyze High-throughput DSF Screenings: HTSDSF Explorer, a tool for DSF screenings

The identification of new drugs for novel therapeutic targets requires the screening of libraries containing tens of thousands of compounds. While experimental screenings are assisted by high-throughput technologies, in target-based biophysical assays, such as differential scanning fluorimetry (DSF), the analysis steps must be calculated manually, often combining several software packages. To simplify the determination of the melting temperature (Tm) of the target and the change induced by ligand binding (?Tm), we developed the HTSDSF explorer, a versatile, all-in-one, user-friendly application suite. Implemented as a server-client application, in the primary screenings, HTSDSF explorer pre-analyzes and displays the Tm and ?Tm results interactively, thereby allowing the user to study hundreds of conditions and select the primary hits in minutes. This application also allows the determination of preliminary binding constants (KD) through a series of subsequent dose–response assays on the primary hits, thereby facilitating the ranking of validated hits and the advance of drug discovery efforts. © 2021 Elsevier Lt

Synthesis of Stable Cholesteryl–Polyethylene Glycol–Peptide Conjugates with Non-Disperse Polyethylene Glycol Lengths

A method for conjugating cholesterol to peptide ligands through non-disperse polyethylene glycol (ND-PEG) through a non-hydrolysable linkage is described. The iterative addition of tetraethylene glycol macrocyclic sulfate to cholesterol (Chol) renders a family of highly pure well-defined Chol-PEG compounds with different PEG lengths from 4 up to 20 ethylene oxide units, stably linked through an ether bond. The conjugation of these Chol-PEG compounds to the cyclic (RGDfK) peptide though Lys5 side chains generates different lengths of Chol-PEG-RGD conjugates that retain the oligomer purity of the precursors, as analysis by HRMS and NMR has shown. Other derivatives were synthesized with similar results, such as Chol-PEG-OCH3 and Chol-PEG conjugated to glutathione and Tf1 peptides through maleimide–thiol chemoselective ligation. This method allows the systematic synthesis of highly pure uniform stable Chol-PEGs, circumventing the use of activation groups on each elongation step and thus reducing the number of synthesis steps.We thank M. Dí az and M. Vilaseca (Mass Spectrometry Core Facility, IRB Barcelona) for the support with the MS data and the Peptide Synthesis Unit (U3) of Nanbiosis ICTS. This work was supported by the Spanish Government (no. RTC-2014- 2207-1, Centers of Excellence Severo Ochoa), CIBER-BBN (Lipocell, no. CB06-01-0074), European Community Horizon 2020 (Smart4Fabry, no. 720942), IRB Barcelona, BBVA foundation (M.J.M.), and Generalitat de Catalunya (nos. 2017-SGR-1439 and 2017-SGR-50 and the CERCA Programme). M.J.M. is an ICREA Programme Investigator.Peer reviewe

Controlling oncogenic KRAS signaling pathways with a Palladium-responsive peptide

RAS oncoproteins are molecular switches associated with critical signaling pathways that regulate cell proliferation and differentiation. Mutations in the RAS family, mainly in the KRAS isoform, are responsible for some of the deadliest cancers, which has made this protein a major target in biomedical research. Here we demonstrate that a designed bis-histidine peptide derived from the αH helix of the cofactor SOS1 binds to KRAS with high affinity upon coordination to Pd(II). NMR spectroscopy and MD studies demonstrate that Pd(II) has a nucleating effect that facilitates the access to the bioactive α-helical conformation. The binding can be suppressed by an external metal chelator and recovered again by the addition of more Pd(II), making this system the first switchable KRAS binder, and demonstrates that folding-upon-binding mechanisms can operate in metal-nucleated peptides. In vitro experiments show that the metallopeptide can efficiently internalize into living cells and inhibit the MAPK kinase cascadeS