Gene Regulation Systems for Gene Therapy Applications in the Central Nervous System

Substantial progress has been made in the development of novel gene therapy strategies for central nervous system (CNS) disorders in recent years. However, unregulated transgene expression is a significant issue limiting human applications due to the potential side effects from excessive levels of transgenic protein that indiscriminately affect both diseased and nondiseased cells. Gene regulation systems are a tool by which tight tissue-specific and temporal regulation of transgene expression may be achieved. This review covers the features of ideal regulatory systems and summarises the mechanics of current exogenous and endogenous gene regulation systems and their utility in the CNS

A model for the study of ligand binding to the ribosomal RNA helix h44.

Oligonucleotide models of ribosomal RNA domains are powerful tools to study the binding and molecular recognition of antibiotics that interfere with bacterial translation. Techniques such as selective chemical modification, fluorescence labeling and mutations are cumbersome for the whole ribosome but readily applicable to model RNAs, which are readily crystallized and often give rise to higher resolution crystal structures suitable for detailed analysis of ligand-RNA interactions. Here, we have investigated the HX RNA construct which contains two adjacent ligand binding regions of helix h44 in 16S ribosomal RNA. High-resolution crystal structure analysis confirmed that the HX RNA is a faithful structural model of the ribosomal target. Solution studies showed that HX RNA carrying a fluorescent 2-aminopurine modification provides a model system that can be used to monitor ligand binding to both the ribosomal decoding site and, through an indirect effect, the hygromycin B interaction region

CMT-3 targets different α-synuclein aggregates mitigating their toxic and inflammogenic effects

Parkinson's disease (PD) is a neurodegenerative disorder for which only symptomatic treatments are available. Repurposing drugs that target α-synuclein aggregation, considered one of the main drivers of PD progression, could accelerate the development of disease-modifying therapies. In this work, we focused on chemically modified tetracycline 3 (CMT-3), a derivative with reduced antibiotic activity that crosses the blood–brain barrier and is pharmacologically safe. We found that CMT-3 inhibited α-synuclein amyloid aggregation and led to the formation of non-toxic molecular species, unlike minocycline. Furthermore, CMT-3 disassembled preformed α-synuclein amyloid fibrils into smaller fragments that were unable to seed in subsequent aggregation reactions. Most interestingly, disaggregated species were non-toxic and less inflammogenic on brain microglial cells. Finally, we modelled the interactions between CMT-3 and α-synuclein aggregates by molecular simulations. In this way, we propose a mechanism for fibril disassembly. Our results place CMT-3 as a potential disease modifier for PD and possibly other synucleinopathies.Fil: González Lizarraga, Maria Florencia. Universidad Nacional de Tucumán. Instituto de Investigaciones En Medicina Molecular y Celular Aplicada del Bicentenario. - Gobierno de la Provincia de Tucumán. Ministerio de Salud. Sistema Provincial de Salud. Instituto de Investigaciones en Medicina Molecular y Celular Aplicada del Bicentenario. - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet Noa Sur. Instituto de Investigaciones en Medicina Molecular y Celular Aplicada del Bicentenario; ArgentinaFil: Ploper, Diego. Universidad Nacional de Tucumán. Instituto de Investigaciones En Medicina Molecular y Celular Aplicada del Bicentenario. - Gobierno de la Provincia de Tucumán. Ministerio de Salud. Sistema Provincial de Salud. Instituto de Investigaciones en Medicina Molecular y Celular Aplicada del Bicentenario. - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet Noa Sur. Instituto de Investigaciones en Medicina Molecular y Celular Aplicada del Bicentenario; ArgentinaFil: Avila, Cesar Luis. Universidad Nacional de Tucumán. Instituto de Investigaciones En Medicina Molecular y Celular Aplicada del Bicentenario. - Gobierno de la Provincia de Tucumán. Ministerio de Salud. Sistema Provincial de Salud. Instituto de Investigaciones en Medicina Molecular y Celular Aplicada del Bicentenario. - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet Noa Sur. Instituto de Investigaciones en Medicina Molecular y Celular Aplicada del Bicentenario; ArgentinaFil: Socias, Sergio Benjamin. Universidad Nacional de Tucumán. Instituto de Investigaciones En Medicina Molecular y Celular Aplicada del Bicentenario. - Gobierno de la Provincia de Tucumán. Ministerio de Salud. Sistema Provincial de Salud. Instituto de Investigaciones en Medicina Molecular y Celular Aplicada del Bicentenario. - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet Noa Sur. Instituto de Investigaciones en Medicina Molecular y Celular Aplicada del Bicentenario; ArgentinaFil: dos Santos Pereira, Mauricio. Universidade de Sao Paulo; BrasilFil: Machín, Belén. Universidad Nacional de Tucumán. Instituto de Investigaciones En Medicina Molecular y Celular Aplicada del Bicentenario. - Gobierno de la Provincia de Tucumán. Ministerio de Salud. Sistema Provincial de Salud. Instituto de Investigaciones en Medicina Molecular y Celular Aplicada del Bicentenario. - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet Noa Sur. Instituto de Investigaciones en Medicina Molecular y Celular Aplicada del Bicentenario; ArgentinaFil: Del Bel, Elaine. Universidade de Sao Paulo; BrasilFil: Michel, Patrick Pierre. Centre National de la Recherche Scientifique; FranciaFil: Pietrasanta, Lia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Física de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Física de Buenos Aires; ArgentinaFil: Raisman Vozari, Rita. Centre National de la Recherche Scientifique; FranciaFil: Chehin, Rosana Nieves. Universidad Nacional de Tucumán. Instituto de Investigaciones En Medicina Molecular y Celular Aplicada del Bicentenario. - Gobierno de la Provincia de Tucumán. Ministerio de Salud. Sistema Provincial de Salud. Instituto de Investigaciones en Medicina Molecular y Celular Aplicada del Bicentenario. - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet Noa Sur. Instituto de Investigaciones en Medicina Molecular y Celular Aplicada del Bicentenario; Argentin

Antiproliferative and antibacterial activity of some glutarimide derivatives

Antiproliferative and antibacterial activities of nine glutarimide derivatives (1–9) were reported. Cytotoxicity of compounds was tested toward three human cancer cell lines, HeLa, K562 and MDA-MB-453 by MTT assay. Compound 7 (2-benzyl-2-azaspiro[5.11]heptadecane-1,3,7-trione), containing 12-membered ketone ring, was found to be the most potent toward all tested cell lines (IC50 = 9–27 μM). Preliminary screening of antibacterial activity by a disk diffusion method showed that Gram-positive bacteria were more susceptible to the tested compounds than Gram-negative bacteria. Minimum inhibitory concentration (MIC) determined by a broth microdilution method confirmed that compounds 1, 2, 4, 6–8 and 9 inhibited the growth of all tested Gram-positive and some of the Gram-negative bacteria. The best antibacterial potential was achieved with compound 9 (ethyl 4-(1-benzyl-2,6-dioxopiperidin-3-yl)butanoate) against Bacillus cereus (MIC 0.625 mg/mL; 1.97 × 10−3 mol/L). Distinction between more and less active/inactive compounds was assessed from the pharmacophoric patterns obtained by molecular interaction fields

Complex macrocycle exploration: parallel, heuristic, and constraint-based conformer generation using ForceGen.

ForceGen is a template-free, non-stochastic approach for 2D to 3D structure generation and conformational elaboration for small molecules, including both non-macrocycles and macrocycles. For conformational search of non-macrocycles, ForceGen is both faster and more accurate than the best of all tested methods on a very large, independently curated benchmark of 2859 PDB ligands. In this study, the primary results are on macrocycles, including results for 431 unique examples from four separate benchmarks. These include complex peptide and peptide-like cases that can form networks of internal hydrogen bonds. By making use of new physical movements ("flips" of near-linear sub-cycles and explicit formation of hydrogen bonds), ForceGen exhibited statistically significantly better performance for overall RMS deviation from experimental coordinates than all other approaches. The algorithmic approach offers natural parallelization across multiple computing-cores. On a modest multi-core workstation, for all but the most complex macrocycles, median wall-clock times were generally under a minute in fast search mode and under 2 min using thorough search. On the most complex cases (roughly cyclic decapeptides and larger) explicit exploration of likely hydrogen bonding networks yielded marked improvements, but with calculation times increasing to several minutes and in some cases to roughly an hour for fast search. In complex cases, utilization of NMR data to constrain conformational search produces accurate conformational ensembles representative of solution state macrocycle behavior. On macrocycles of typical complexity (up to 21 rotatable macrocyclic and exocyclic bonds), design-focused macrocycle optimization can be practically supported by computational chemistry at interactive time-scales, with conformational ensemble accuracy equaling what is seen with non-macrocyclic ligands. For more complex macrocycles, inclusion of sparse biophysical data is a helpful adjunct to computation

Building Enhancers from the Ground Up: A Synthetic Biology Approach

A challenge of the synthetic biology approach is to use our understanding of a system to recreate a biological function with specific properties. We have applied this framework to bacterial enhancers, combining a driver, transcription factor binding sites, and a poised polymerase to create synthetic modular enhancers. Our findings suggest that enhancer-based transcriptional control depends critically and quantitatively on DNA looping, leading to complex regulatory effects when the enhancer cassettes contain additional transcription factor binding sites for TetR, a bacterial transcription factor. We show through a systematic interplay of experiment and thermodynamic modeling that the level of gene expression can be modulated to convert a variable inducer concentration input into discrete or step-like output expression levels. Finally, using a different DNA-binding protein (TraR), we show that the regulatory output is not a particular feature of the specific DNA-binding protein used for the enhancer but a general property of synthetic bacterial enhancers

In silico strategies on prion pathogenic conversion and inhibition from PrPC -PrPSc

Published ArticleTo date, various therapeutic strategies identified numerous anti-prion compounds and antibodies that stabilize PrPC, block the conversion of PrPC-PrPSc and increased effect on PrPSc clearance. However, no suitable drug has been identified clinically so far due to the poor oral absorption, low blood-brain-barrier [BBB] penetration, and high toxicity. Although some of the drugs were proven to be effective in prion-infected cell culture and whole animal models, none of them increased the rate of survival compared to placebo. Areas covered: In this review, the authors highlight the importance of in silico approaches like molecular docking, virtual screening, pharmacophore analysis, molecular dynamics, QSAR, CoMFA and CoMSIA applied to detect molecular mechanisms of prion inhibition and conversion from PrPC-PrPSc. Expert opinion: Several in silico approaches combined with experimental studies have provided many structural and functional clues on the stability and physiological activity of prion mutants. Further, various studies of in silico and in vivo approaches were also shown to identify several new small organic anti-scrapie compounds to decrease the accumulation of PrPres in cell culture, inhibit the aggregation of a PrPC peptide, and possess pharmacokinetic characteristics that confirm the drug-likeness of these compounds

THE GATING OF THE BACTERIAL MECHANOSENSITIVE CHANNEL MSCS REFLECTS ITS FUNCTION AS A SENSOR OF BOTH CROWDING AND LATERAL PRESSURE AS WELL AS ITS ROLE IN OSMOREGULATION

The mechanosensitive channel MscS is a ubiquitous bacterial membrane valve that opens by increased tension in the event of osmotic down-shock, releasing small internal osmolytes and thus preventing the cell from excessive hydration and possible lysis. This osmolyte release is accompanied by a reduction of osmotic pressure and volume of the cell, which simultaneously increases crowding. The large catalogue of MscS homologs in both prokaryotes and eukaryotes makes the study of this channel enticing to the field of physical biochemistry. Here are the results of three different studies, two of which focus on the gating of MscS in the presence of large osmolytes and amphipathic compounds and a third which describes the first electrophysiological examination of the inner membrane of the facultative pathogen Vibrio cholerae. The first study in Chapter 2 describes the sensitivity of gating transitions in MscS to large intracellular macromolecules. This sensitivity originates at the cytoplasmic cage domain and the perceived crowding alters the rate of opening, closing and inactivation. Chapter 3 details the utilization of MscS as a sensor for changes in the lateral pressure profile of native bilayers and how this technique can be used to resolve the potential of antibacterial agents to partition into the membrane. The third and final study describes our development of a procedure to generate giant spheroplasts of Vibrio cholerae and the subsequent characterization of its two major mechanosensitive channels in terms of gating, inactivation, conductivity, and compatible osmolyte sensitivity as well as the durability of the pathogen in response to osmotic shock. These contributions to the field of mechanobiology and channel biophysics suggest that environmental feedback during osmoregulation is recognized by the cell, provide a potential method to monitor the partitioning of antibiotics into a cell membrane, and lastly detail the mechano-electrical response of a relevant, disease-causing bacteria