Predicting structural determinants and Ligand poses in proteins involved in neurological diseases: bioinformatics and molecular simulation studies

Part I presents the computational tools used in this work: the comparative modeling and molecular docking approaches along with molecular dynamics. Part II presents structural predictions of Ca2+-binding domains in Ca2+-gated channels. A detailed description of the structure and function of these proteins can be found in the following Chapters. Chapter 4 focuses on human large conductance Ca2+- and voltage-gated potassium channel (hBKCa). Bioinformatics approaches and MD simulations were used to construct models of two domains important for Ca2+ binding and channel gating, namely the Regulator of Conductance for K+ (RCK1) and the so called calcium bowl. The relevance of these models for interpreting the available molecular biology data is then discussed. Chapter 5 deals with bestrophins, a recently discovered family of Cl 12 channels. Bestrophins feature a well conserved Asp-rich tract in their C-terminal part, which is homologous to Ca2+-binding motifs in calcium bowl of hBKCa. Based on these considerations, we constructed homology models of human bestrophin-1 Asp-rich domain. MD simulations and free energy calculations were used to identify Asp and Glu residues binding Ca2+ and to predict eects of their mutations to Ala. My work, performed in collaboration with C. Anselmi (SISSA/ISAS), was complemented by free energy calculations carried out by F. Pietrucci (SISSA/ISAS). Selected mutations were investigated by electrophysiological experiments performed by Prof. A. Menini, J. Rievaj, F. W. Grillo, and A. Boccaccio (SISSA/ISAS). The model of Asp-rich domain was then validated against experimental results. Part III is devoted to the prion protein. In this Part, Chapter 6 presents in vitro studies of D18scFv anti-prion effects performed by groups of Prof. C. Zurzolo (Institut Pasteur, Paris, France), Prof. G. Legname (SISSA/ISAS), L. Zentilin and M. Giacca (ICGEB, Trieste, Italy) and by Prof. S. B. Prusiner (Institute for Neurodegenerative Diseases, University of California San Francisco, U.S.A.) and structural prediction of a complex between the small antibody fragment (D18scFv) and PrPC. The complex was modeled using bioinformatics approaches. Initially, the D18scFv fragment alone was modeled based on a similar antibody-fragment template and then docked with prion protein. Based on this, interactions relevant for the recognition between the two proteins and for the mechanism of action of D18scFv are discussed. Chapter 7 describes a computational protocol for the design of ligands targeting cavity-less proteins, like most proteins involved in neurodegenerative diseases. Molecular docking methods are combined with MD simulations and free energy calculations using the metadynamics method [33, 34] to gain insights in ligand binding to such proteins, in our case to prion protein. We focused on a compound showing antiprion activity in vitro. Ligand-target interactions and ligand binding affinity as emerged by using our approach are compared with the available NMR data [35] and experimental constant of dissociation [35]. In this work, also other two students and one postdoc were involved beside myself, namely S. Bongarzone, G. Rossetti and X. Biarnes (SISSA/ISAS). Finally, the conclusions are drawn in the last Chapter. The thesis closes with the List of publications and with the Acknowledgments

Modulation of Alpha-Synuclein Aggregation by Dopamine Analogs

The action of dopamine on the aggregation of the unstructured alpha-synuclein (α-syn) protein may be linked to the pathogenesis of Parkinson's disease. Dopamine and its oxidation derivatives may inhibit α-syn aggregation by non-covalent binding. Exploiting this fact, we applied an integrated computational and experimental approach to find alternative ligands that might modulate the fibrillization of α-syn. Ligands structurally and electrostatically similar to dopamine were screened from an established library. Five analogs were selected for in vitro experimentation from the similarity ranked list of analogs. Molecular dynamics simulations showed they were, like dopamine, binding non-covalently to α-syn and, although much weaker than dopamine, they shared some of its binding properties. In vitro fibrillization assays were performed on these five dopamine analogs. Consistent with our predictions, analyses by atomic force and transmission electron microscopy revealed that all of the selected ligands affected the aggregation process, albeit to a varying and lesser extent than dopamine, used as the control ligand. The in silico/in vitro approach presented here emerges as a possible strategy for identifying ligands interfering with such a complex process as the fibrillization of an unstructured protein

Regulation of Bestrophins by Ca2+: A Theoretical and Experimental Study

Bestrophins are a recently discovered family of Cl− channels, for which no structural information is available. Some family members are activated by increased intracellular Ca2+ concentration. Bestrophins feature a well conserved Asp-rich tract in their COOH terminus (Asp-rich domain), which is homologous to Ca2+-binding motifs in human thrombospondins and in human big-conductance Ca2+- and voltage-gated K+ channels (BKCa). Consequently, the Asp-rich domain is also a candidate for Ca2+ binding in bestrophins. Based on these considerations, we constructed homology models of human bestrophin-1 (Best1) Asp-rich domain using human thrombospondin-1 X-ray structure as a template. Molecular dynamics simulations were used to identify Asp and Glu residues binding Ca2+ and to predict the effects of their mutations to alanine. We then proceeded to test selected mutations in the Asp-rich domain of the highly homologous mouse bestrophin-2. The mutants expressed in HEK-293 cells were investigated by electrophysiological experiments using the whole-cell voltage-clamp technique. Based on our molecular modeling results, we predicted that Asp-rich domain has two defined binding sites and that D301A and D304A mutations may impact the binding of the metal ions. The experiments confirmed that these mutations do actually affect the function of the protein causing a large decrease in the Ca2+-activated Cl− current, fully consistent with our predictions. In addition, other studied mutations (E306A, D312A) did not decrease Ca2+-activated Cl− current in agreement with modeling results

HIV-1 Protease Dimerization Dynamics Reveals a Transient Druggable Binding Pocket at the Interface

International audienceThe binding mechanism of HIV-1 protease monomers leading to the catalytically competent dimeric enzyme has been investigated by means of state-of-the-art atomistic simulations. The emerging picture allows a deeper understanding of experimental observations and reveals that water molecules trapped at the interface have an important role in slowing down the kinetics of the association process. Unexpectedly, a cryptic binding pocket is identified at the interface of the complex, corresponding to a partially bound dimer that lacks enzymatic function. The pocket has a transient nature with a lifetime longer than 1 μs, and it displays very favorable druggability features. Docking as well as MM-GBSA free-energy calculations further support the possibility to target the new binding site by means of inhibitors able to prevent the complete dimerization by capturing the inactive conformation. This discovery could open the way to the rational design of a new class of anti-HIV drugs

Structural Space of the Duffy Antigen/Receptor for Chemokines’ Intrinsically Disordered Ectodomain 1 Explored by Temperature Replica-Exchange Molecular Dynamics Simulations

International audiencePlasmodium vivax malaria affects 14 million people each year. Its invasion requires interactions between the parasitic Duffy-binding protein (PvDBP) and the N-terminal extracellular domain (ECD1) of the host’s Duffy antigen/receptor for chemokines (DARC). ECD1 is highly flexible and intrinsically disordered, therefore it can adopt different conformations. We computationally modeled the challenging ECD1 local structure. With T-REMD simulations, we sampled its dynamic behavior and collected its most representative conformations. Our results suggest that most of the DARC ECD1 domain remains in a disordered state during the simulated time. Globular local conformations are found in the analyzed local free-energy minima. These globular conformations share an α-helix spanning residues Ser18 to Ser29 and in many cases they comprise an antiparallel β-sheet, whose β-strands are formed around residues Leu10 and Ala49. The formation of a parallel β-sheet is almost negligible. So far, progress in understanding the mechanisms forming the basis of the P. vivax malaria infection of reticulocytes has been hampered by experimental difficulties, along with a lack of DARC structural information. Our collection of the most probable ECD1 structural conformations will help to advance modeling of the DARC structure and to explore DARC–ECD1 interactions with a range of physiological and pathological ligands

The Interplay of Cholesterol and Ligand Binding in hTSPO from Classical Molecular Dynamics Simulations

The translocator protein (TSPO) is a 18kDa transmembrane protein, ubiquitously present in human mitochondria. It is overexpressed in tumor cells and at the sites of neuroinflammation, thus representing an important biomarker, as well as a promising drug target. In mammalian TSPO, there are cholesterol–binding motifs, as well as a binding cavity able to accommodate different chemical compounds. Given the lack of structural information for the human protein, we built a model of human (h) TSPO in the apo state and in complex with PK11195, a molecule routinely used in positron emission tomography (PET) for imaging of neuroinflammatory sites. To better understand the interactions of PK11195 and cholesterol with this pharmacologically relevant protein, we ran molecular dynamics simulations of the apo and holo proteins embedded in a model membrane. We found that: (i) PK11195 stabilizes hTSPO structural fold; (ii) PK11195 might enter in the binding site through transmembrane helices I and II of hTSPO; (iii) PK11195 reduces the frequency of cholesterol binding to the lower, N–terminal part of hTSPO in the inner membrane leaflet, while this impact is less pronounced for the upper, C–terminal part in the outer membrane leaflet, where the ligand binding site is located; (iv) very interestingly, cholesterol most frequently binds simultaneously to the so-called CRAC and CARC regions in TM V in the free form (residues L150–X–Y152–X(3)–R156 and R135–X(2)–Y138–X(2)–L141, respectively). However, when the protein is in complex with PK11195, cholesterol binds equally frequently to the CRAC–resembling motif that we observed in TM I (residues L17–X(2)–F20–X(3)–R24) and to CRAC in TM V. We expect that the CRAC–like motif in TM I will be of interest in future experimental investigations. Thus, our MD simulations provide insight into the structural features of hTSPO and the previously unknown interplay between PK11195 and cholesterol interactions with this pharmacologically relevant protein

Identification of Anti-Mycobacterium and Anti-Legionella Compounds With Potential Distinctive Structural Scaffolds From an HD-PBL Using Phenotypic Screens in Amoebae Host Models

Tubercular Mycobacteria and Legionella pneumophila are the causative agents of potentially fatal respiratory diseases due to their intrinsic pathogenesis but also due to the emergence of antibiotic resistance that limits treatment options. The aim of our study was to explore the antimicrobial activity of a small ligand-based chemical library of 1255 structurally diverse compounds. These compounds were screened in a combination of three assays, two monitoring the intracellular growth of the pathogenic bacteria, Mycobacterium marinum and L. pneumophila, and one assessing virulence of M. marinum. We set up these assays using two amoeba strains, the genetically tractable social amoeba Dictyostelium discoideum and the free-living amoeba Acanthamoeba castellanii. In summary, 64 (5.1%) compounds showed anti-infective/anti-virulence activity in at least one of the three assays. The intracellular assays hit rate varied between 1.7% (n = 22) for M. marinum and 2.8% (n = 35) for L. pneumophila with seven compounds in common for both pathogens. In parallel, 1.2% (n = 15) of the tested compounds were able to restore D. discoideum growth in the presence of M. marinum spiked in a lawn of food bacteria. We also validated the generality of the hits identified in the A. castellanii-M. marinum anti-infective screen using the D. discoideum-M. marinum host-pathogen model. The characterization of anti-infective and antibacterial hits in the latter infection model revealed compounds able to reduce intracellular growth more than 50% at 30 μM. Moreover, the chemical space and physico-chemical properties of the anti-M. marinum hits were compared to standard and candidate Mycobacterium tuberculosis (Mtb) drugs using ChemGPS-NP. A principle component analysis identified separate clusters for anti-M. marinum and anti-L. pneumophila hits unveiling the potentially new physico-chemical properties of these hits compared to standard and candidate M. tuberculosis drugs. Our studies underscore the relevance of using a combination of low-cost and low-complexity assays with full 3R compliance in concert with a rationalized focused library of compounds to identify new chemical scaffolds and to dissect some of their properties prior to taking further steps toward compound development

Development of antibody fragments for immunotherapy of prion diseases

International audiencePrions are infectious proteins responsible for a group of fatal neurodegenerative diseases called transmissible spongiform encephalopathies (TSEs), or prion diseases. In mammals, prions reproduce themselves by recruiting the normal cellular protein (PrPC) and inducing its conversion to the disease-causing isoform denominated PrPSc. Recently, anti-prion antibodies have been shown to permanently cure prion-infected cells. However, the inability of full-lenght antibodies and proteins to cross the blood-brain barrier (BBB) hampers their use in the therapy of TSEs in vivo. Alternatively, brain delivery of prion-specific scFv by adeno-associated virus (AAV) transfer delays the onset of the disease in infected mice, although protection is not complete. We investigated the anti-prion effects of a recombinant anti-PrP (D18) single-chain variable fragment (scFv) by direct addition to scrapie infected cell cultures or by infection with both lentivirus and adeno-associated virus (AAV) transducing vectors. We show that recombinant anti-PrP scFv is able to reduce proteinase K-resistant PrP content in infected cells. In addition, we demonstrate that lentiviruses are more efficient than AAV in gene transferring of the anti-PrP scFv gene and in reducing PrPSc content in infected neuronal cell lines. Finally, we have used a bioinformatic approach to construct a structural model of D18scFv-PrPC complex. Interestingly, according to the docking results, ArgPrP151 (Arg151 from prion protein) is the key residue for the interactions with D18scFv, anchoring the PrPC to the cavity of the antibody. Taken together, these results indicate that combined passive and active immunotherapy targeting PrP might be promising strategies for therapeutic intervention in prion diseases