Protein-ligand binding with the coarse-grained Martini model

The detailed understanding of the binding of small molecules to proteins is the key for the development of novel drugs or to increase the acceptance of substrates by enzymes. Nowadays, computer-aided design of protein–ligand binding is an important tool to accomplish this task. Current approaches typically rely on high-throughput docking essays or computationally expensive atomistic molecular dynamics simulations. Here, we present an approach to use the recently re-parametrized coarse-grained Martini model to perform unbiased millisecond sampling of protein–ligand interactions of small drug-like molecules. Remarkably, we achieve high accuracy without the need of any a priori knowledge of binding pockets or pathways. Our approach is applied to a range of systems from the well-characterized T4 lysozyme over members of the GPCR family and nuclear receptors to a variety of enzymes. The presented results open the way to high-throughput screening of ligand libraries or protein mutations using the coarse-grained Martini model

Discovery of a Potent and Orally Active Dual GPBAR1/CysLT1R Modulator for the Treatment of Metabolic Fatty Liver Disease

Nonalcoholic fatty liver disease (NAFLD) and nonalcoholic steatohepatitis (NASH) are two highly prevalent human diseases caused by excessive fat deposition in the liver. Although multiple approaches have been suggested, NAFLD/NASH remains an unmet clinical need. Here, we report the discovery of a novel class of hybrid molecules designed to function as cysteinyl leukotriene receptor 1 (CysLT1R) antagonists and G protein bile acid receptor 1 (GPBAR1/TGR5) agonists for the treatment of NAFLD/NASH. The most potent of these compounds generated by harnessing the scaffold of the previously described CystLT1R antagonists showed efficacy in reversing liver histopathology features in a preclinical model of NASH, reshaping the liver transcriptome and the lipid and energy metabolism in the liver and adipose tissues. In summary, the present study described a novel orally active dual CysLT1R antagonist/GPBAR1 agonist that effectively protects against the development of NAFLD/NASH, showing promise for further development

Structural basis of dimerization of chemokine receptors CCR5 and CXCR4

This is the minimum dataset of the Nature Communication paper "Structural basis of dimerization of chemokine receptors CCR5 and CXCR4". This repository is composed of two zipped archives. The first archive, "Dataset Minimum", contains all the trajectories, force field parameters, input files and analyses generated for this work. All relevant information about the specific nature and content of the files in the dataset and its organization is reported in the README files provided inside it. The second archive, "Source Data", contains only the raw data used to assemble the figures shown in the work. This data is also stored in the Dataset Minimum archive. The files are divided into different folders according to the image they belong to. Each folder is divided into subfolders to distinguish the data reported in each image panel. Most files can be read using Excel or a word processor such as WordPad, NotePad, or Notepad++. Structure files are provided in the pdb format and can be read using software like VMD, Pymol, or Chimera. Abstract G protein coupled receptors (GPCRs) are prominent drug targets responsible for extracellular-to-intracellular signal transduction. GPCRs can form functional dimers that have been poorly characterized so far. Here, we show the dimerization mechanism of the chemokine receptors CCR5 and CXCR4 by means of an advanced free-energy technique named coarse-grained metadynamics. Our results reproduce binding events between the GPCRs occurring in the minute timescale - the longest ever simulated - which reveal a symmetric and an asymmetric dimeric structure for each of the three investigated systems, CCR5/CCR5, CXCR4/CXCR4 and CCR5/CXCR4. The transmembrane helices TM4-TM5 and TM6-TM7 are the preferred binding interfaces for CCR5 and CXCR4, respectively. The identified dimer states differ in the access to the binding sites of the ligand and G protein, indicating that dimerization represents a fine allosteric mechanism to regulate receptor activity. Our study offers unprecedented structural bases for the design of ligands able to modulate the formation of CCR5 and CXCR4 dimers and in turn their activity, with therapeutic potential against HIV, cancer and immune-inflammatory diseases.This work has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme ("CoMMBi" ERC grant agreement No.101001784). V.L. especially acknowledges the multi-year support by a grant from the Swiss National Supercomputing Centre (CSCS) under project IDs s1150 and u8, while the funding from "Partnership for Advanced Computing in Europe" (PRACE) (call 16 with project ID 2016153685) was discontinued only after the first year based on the decision of the 2018 PRACE Access Committee and PRACE Board of Directors, which caused delay in research. We also thank the NVIDIA Corporation for the donation of a Tesla K40 GPU. D.D. acknowledges the support of the Italian Foundation for Cancer Research AIRC (Project No. IG 2022 ID 27534)

Molecular Dynamics Simulations of the Host Defense Peptide Temporin L and Its Q3K Derivative: An Atomic Level View from Aggregation in Water to Bilayer Perturbation

Temporin L (TempL) is a 13 residue Host Defense Peptide (HDP) isolated from the skin of frogs. It has a strong affinity for lipopolysaccharides (LPS), which is related to its high activity against Gram-negative bacteria and also to its strong tendency to neutralize the pro-inflammatory response caused by LPS release from inactivated bacteria. A designed analog with the Q3K substitution shows an enhancement in both these activities. In the present paper, Molecular Dynamics (MD) simulations have been used to investigate the origin of these improved properties. To this end, we have studied the behavior of the peptides both in water solution and in the presence of LPS lipid-A bilayers, demonstrating that the main effect through which the Q3K substitution improves the peptide activities is the destabilization of peptide aggregates in water

Behavior of a Peptide During a Langmuir–Blodgett Compression Isotherm: A Molecular Dynamics Simulation Study

A detailed characterization of the behavior of the amphiphilic antimicrobial peptide Trichogin GA IV (TRIC) at the air/water interface during a Langmuir–Blodgett (LB) isotherm is reported. By means of molecular dynamics simulations, experimental data are explained in terms of the conformational changes and aggregate features adopted by TRIC. We show that, due to compression, different structural changes occur: initially formed drop-like aggregates coalesce, forming nanofibers; on increasing the surface tension further, these nanofibers constitute a web-like structure in which meshes are filled by water pools. During these transitions, the peptide chains lie almost parallel to the surface mostly adopting a helical conformation. At high peptide concentration, reaching the maximum of the allowed surface pressure, a monolayer of TRICs in nonhelical conformation and vertically aligned with respect to the air/water interface is formed

The Influence of pH on the Scleroglucan and Scleroglucan/Borax Systems

The effects that an increase of environmental pH has on the triple helix of scleroglucan (Sclg) and on the Sclg/borax hydrogel are reported. Rheological experiments show that the hydrogel is less sensitive to pH increase than Sclg alone, while at pH = 14 a dramatic viscosity decrease takes place for both systems. This effect is evidenced also by the reduced water uptake and anisotropic elongation detected, at pH = 14, by the swelling behaviour of tablets prepared with the Sclg/borax system. On the opposite, a different behaviour was observed with guar gum and locust bean gum tablets, tested as reference polysaccharides. The effect of pH on the structure of Sclg and Sclg/borax was investigated also by means of spectroscopic approaches based on the interaction between Congo red (CR) and the Sclg triple helix. Obtained results indicated that the CR absorbance maximum is shifted as a function of pH and by the presence of borax. Principal component analysis allowed very precise identification of the pH value at which the Sclg helix collapses. Molecular dynamics simulations of the Sclg/borax–CR complex indicated that, at physiological pH, only a few ordered configurations are populated, according to the induced circular dichroism (CD) spectrum evidence

Ubiquitylation of BBSome is required for ciliary assembly and signaling

Bardet-Biedl syndrome (BBS) is a ciliopathy characterized by retinal degeneration, obesity, renal abnormalities, postaxial polydactyly, and developmental defects. Genes mutated in BBS encode for components and regulators of the BBSome, an octameric complex that controls the trafficking of cargos and receptors within the primary cilium. Although both structure and function of the BBSome have been extensively studied, the impact of ubiquitin signaling on BBSome is largely unknown. We identify the E3 ubiquitin ligase PJA2 as a novel resident of the ciliary compartment and regulator of the BBSome. Upon GPCR-cAMP stimulation, PJA2 ubiquitylates BBSome subunits. We demonstrate that ubiquitylation of BBS1 at lysine 143 increases the stability of the BBSome and promotes its binding to BBS3, an Arf-like GTPase protein controlling the targeting of the BBSome to the ciliary membrane. Downregulation of PJA2 or expression of a ubiquitylation-defective BBS1 mutant (BBS1 K143R) affects the trafficking of G-proteincoupled receptors (GPCRs) and Shh-dependent gene transcription. Expression of BBS1 K143R in vivo impairs cilium formation, embryonic development, and photoreceptors' morphogenesis, thus recapitulating the BBS phenotype in the medaka fish model