Preparation and Use of a General Solid-Phase Intermediate to Biomimetic Scaffolds and Peptide Condensations

The Distributed Drug Discovery (D3) program develops simple, powerful, and reproducible procedures to enable the distributed synthesis of large numbers of potential drugs for neglected diseases. The synthetic protocols are solid-phase based and inspired by published work. One promising article reported that many biomimetic molecules based on diverse scaffolds with three or more sites of variable substitution can be synthesized in one or two steps from a common key aldehyde intermediate. This intermediate was prepared by the ozonolysis of a precursor functionalized at two variable sites, restricting their presence in the subsequently formed scaffolds to ozone compatible functional groups. To broaden the scope of the groups available at one of these variable sites, we developed a synthetic route to an alternative, orthogonally protected key intermediate that allows the incorporation of ozone sensitive groups after the ozonolysis step. The utility of this orthogonally protected intermediate is demonstrated in the synthesis of several representative biomimetic scaffolds containing ozonolytically labile functional groups. It is compatible with traditional Fmoc peptide chemistry, permitting it to incorporate peptide fragments for use in fragment condensations with peptides containing cysteine at the N-terminus. Overall yields for its synthesis and utilization (as many as 13 steps) indicate good conversions at each step

VERSATILE FMOC-ACETAL MERRIFIELD RESINS: SYNTHESES OF BICYCLIC LACTAMS & LACTONES

poster abstractThe preparation of Merrifield resins 5, which represent versatile intermediates in the syntheses of lactones, lactams, and bicyclic, tricyclic, and tetracyclic scaffolds, is described. The presence of Fmoc and acetal protecting groups allows for the eventual incorporation of ozone-labile groups at R2 (as in III) such as alkenes, alkynes, electron-rich aromatics and pi-excessive heterocycles whereas the previously reported route can only accommodate ozone-compatible groups. An extension of the current methodology to include bicyclic lactams, which features elaboration at each of R1, R2, and R3 of III including fragment condensation examples 10a-c, is described. In all cases separation and characterization of two of the four possible diastereomers was achieved. Using 2-D NMR methods the relative configuration of the two diastereomers is being established. Structures such as III are of interest since the thiazabicycloalkane ring system is a known bioactive scaffold that mimics the beta-turn (reverse turn) in polypeptides and proteins

Reducing dementia risk by targeting modifiable risk factors in mid-life: study protocol for the Innovative midlife intervention for dementia deterrence (In-MINDD) randomised controlled feasibility trial

Background Dementia prevalence is increasing as populations live longer, with no cure and the costs of caring exceeding many other conditions. There is increasing evidence for modifiable risk factors which, if addressed in mid-life, can reduce the risk of developing dementia in later life. These include physical inactivity, low cognitive activity, mid-life obesity, high blood pressure, and high cholesterol. This study aims to assess the acceptability and feasibility and impact of giving those in mid-life, aged between 40 and 60 years, an individualised dementia risk modification score and profile and access to personalised on-line health information and goal setting in order to support the behaviour change required to reduce such dementia risk. A secondary aim is to understand participants’ and practitioners’ views of dementia prevention and explore the acceptability and integration of the Innovative Midlife Intervention for Dementia Deterrence (In-MINDD) intervention into daily life and routine practice. Methods/design In-MINDD is a multi-centre, primary care-based, single-blinded randomised controlled feasibility trial currently being conducted in four European countries (France, Ireland, the Netherlands and the UK). Participants are being recruited from participating general practices. Inclusion criteria will include age between 40 and 60 years; at least one modifiable risk factor for dementia risk (including diabetes, hypertension, obesity, renal dysfunction, current smoker, raised cholesterol, coronary heart disease, current or previous history of depression, self-reported sedentary lifestyle, and self-reported low cognitive activity) access to the Internet. Primary outcome measure will be a change in dementia risk modification score over the timescale of the trial (6 months). A qualitative process evaluation will interview a sample of participants and practitioners about their views on the acceptability and feasibility of the trial and the links between modifiable risk factors and dementia prevention. This work will be underpinned by Normalisation Process Theory. Discussion This study will explore the feasibility and acceptability of a risk profiler and on-line support environment to help individuals in mid-life assess their risk of developing dementia in later life and to take steps to alleviate that risk by tackling health-related behaviour change. Testing the intervention in a robust and theoretically informed manner will inform the development of a future, full-scale randomised controlled trial

Unexpected Hydrolytic Instability of N-Acylated Amino Acid Amides and Peptides

Remote amide bonds in simple N-acyl amino acid amide or peptide derivatives 1 can be surprisingly unstable hydrolytically, affording, in solution, variable amounts of 3 under mild acidic conditions, such as trifluoroacetic acid/water mixtures at room temperature. This observation has important implications for the synthesis of this class of compounds, which includes N-terminal-acylated peptides. We describe the factors contributing to this instability and how to predict and control it. The instability is a function of the remote acyl group, R2CO, four bonds away from the site of hydrolysis. Electron-rich acyl R2 groups accelerate this reaction. In the case of acyl groups derived from substituted aromatic carboxylic acids, the acceleration is predictable from the substituent’s Hammett σ value. N-Acyl dipeptides are also hydrolyzed under typical cleavage conditions. This suggests that unwanted peptide truncation may occur during synthesis or prolonged standing in solution when dipeptides or longer peptides are acylated on the N-terminus with electron-rich aromatic groups. When amide hydrolysis is an undesired secondary reaction, as can be the case in the trifluoroacetic acid-catalyzed cleavage of amino acid amide or peptide derivatives 1 from solid-phase resins, conditions are provided to minimize that hydrolysis

Solid-Phase Synthesis of Arylpiperazine Derivatives and Implementation of the Distributed Drug Discovery (D3) Project in the Search for CNS Agents

We have successfully implemented the concept of Distributed Drug Discovery (D3) in the search for CNS agents. Herein, we demonstrate, for the first time, student engagement from different sites around the globe in the development of new biologically active compounds. As an outcome we have synthesized a 24-membered library of arylpiperazine derivatives targeted to 5-HT1A and 5-HT2A receptors. The synthesis was simultaneously performed on BAL-MBHA-PS resin in Poland and the United States, and on BAL-PS-SynPhase Lanterns in France. The D3 project strategy opens the possibility of obtaining potent 5-HT1A/5-HT2A agents in a distributed fashion. While the biological testing is still centralized, this combination of distributed synthesis with screening will enable a D3 network of students world-wide to participate, as part of their education, in the synthesis and testing of this class of biologically active compounds

Aminolytic Cleavage from Wang Resin. A New Distributed Drug Discovery Laboratory for the Undergraduate Curriculum

poster abstractWhen treated with ammonia or methylamine, unnatural amino acids bound to Wang resin (1) are released as their corresponding amides 2 in good yield and purity. When carried out at room temperature, aminolytic cleavage proceeds slowly with a four-day exposure to ammonia in methanol representing an optimal reaction time. Aminolytic cleavage proceeds well with unhindered primary amines, however, the hindered amine isopropylamine and benzylamines are unacceptably slow to effect cleavage. Use of the secondary amine pyrrolidine led to a complex mixture. Due to the large stoichiometric amine excess required, the scope is currently limited to unhindered, volatile, primary amines. The overall synthesis of 2 from BPI-Gly-Wang resin represents a new Distributed Drug Discovery Laboratory (D3-7) and was rolled out to the spring 2016 Organic II laboratory

The Synthesis and Biological Activity of N-Acylated Amino Acids. A Collaborative Effort of Distributed Drug Discovery (D3)

poster abstractAs part of a Distributed Drug Discovery collaborative effort between students at IUPUI and Medical University of Lublin (Poland), the solid-phase combinatorial synthesis of a series of natural, acylated tyrosine (1) and phenylalanine (2) analogs was carried out in replicated fashion. The crude samples were purified and characterized by LC/MS, proton NMR, and in cases involving novel structures, by proton and carbon-13 NMR and high-resolution mass spectrometry. The samples were characterized in biological assays at the Medical University of Lublin against the Gram-positive bacteria Staphylococcus aureus ATCC 25923, Staphylococcus epidermidis ATCC 12228, Bacillus cereus ATCC 10876, Bacillus subtilis ATCC 10876, and Micrococcus luteus ATCC 10240. Although activity of the 2-nitro and 3-nitro derivatives of phenylalanine was not reproduced by the IUPUI samples, the 5-chlorosalicylic acid derivative 1g demonstrated good activity against M. luteus (MIC = 62.5 g/mL) and moderate activity against S. aureus, S. epidermidis, and B. cereus. O Cl OH HN OH OH O O Ar HN X OH O 1 X = OH 2 X = H 1

On TCR binding predictors failing to generalize to unseen peptides

Several recent studies investigate TCR-peptide/-pMHC binding prediction using machine learning or deep learning approaches. Many of these methods achieve impressive results on test sets, which include peptide sequences that are also included in the training set. In this work, we investigate how state-of-the-art deep learning models for TCR-peptide/-pMHC binding prediction generalize to unseen peptides. We create a dataset including positive samples from IEDB, VDJdb, McPAS-TCR, and the MIRA set, as well as negative samples from both randomization and 10X Genomics assays. We name this collection of samples TChard. We propose the hard split, a simple heuristic for training/test split, which ensures that test samples exclusively present peptides that do not belong to the training set. We investigate the effect of different training/test splitting techniques on the models’ test performance, as well as the effect of training and testing the models using mismatched negative samples generated randomly, in addition to the negative samples derived from assays. Our results show that modern deep learning methods fail to generalize to unseen peptides. We provide an explanation why this happens and verify our hypothesis on the TChard dataset. We then conclude that robust prediction of TCR recognition is still far for being solved

The Bs20x22 anti-CD20-CD22 bispecific antibody has more lymphomacidal activity than do the parent antibodies alone

Previous studies have shown that bispecific antibodies that target both CD20 and CD22 have in vivo lymphomacidal properties. We developed a CD20-CD22 bispecific antibody (Bs20x22) from anti-CD20 and the anti-CD22 monoclonal antibodies (mAb), rituximab and HB22.7, respectively. Bs20x22 was constructed using standard methods and was shown to specifically bind CD20 and CD22. In vitro cytotoxicity assays showed that Bs20x22 was three times more effective than either parent mAb alone and twice as effective as a combination of both parent mAb used at equimolar concentrations. Bs20x22 was also nearly four times more effective at inducing apoptosis than either mAb alone. Examination of the MAPK and SAPK signaling cascades revealed that Bs20x22 induced significantly more p38 phosphorylation than either mAb alone. In an in vivo human NHL xenograft model, treatment with Bs20x22 resulted in significantly greater tumor shrinkage and improved overall survival when compared to either mAb alone or treatment with a combination of HB22.7 and rituximab. The effect of the initial tumor volume was assessed by comparing the efficacy of Bs20x22 administered before xenografts grew versus treatment of established tumors; significantly, greater efficacy was found when treatment was initiated before tumors could become established

Linear/circular spectropolarimetry of diffuse interstellar bands

Context. The identification of the carriers of diffuse interstellar bands (DIBs) remains one of the long-standing mysteries in astronomy. The detection of a polarisation signal in a DIB profile can be used to distinguish between a dust or gas-phase carrier. The polarisation profile can give additional information on the grain or molecular properties of the absorber. In order to detect and measure the linear and circular polarisation of the DIBs we observed reddened lines of sight showing continuum polarisation. For this study we selected two stars HD 197770 and HD 194279. We used high-resolution (R~64.000) spectropolarimetry in the wavelength range from 3700 to 10480 Angstrom with the ESPaDOnS echelle spectrograph mounted at the CFHT. Results. High S/N and high resolution Stokes V (circular), Q and U (linear) spectra were obtained. We constrained upper limits by a factor of 10 for previously observed DIBs. Furthermore, we analysed ~30 additional DIBs for which no spectropolarimetry data has been obtained before. This included the 9577 A DIB and the 8621 A DIB. Conclusions. The lack of polarisation in 45 DIB profiles suggests that none of the absorption lines is induced by a grain-type carrier. The strict upper limits, less than ~0.01%, derived for the observed lines-of-sight imply that if DIBs are due to gas-phase molecules these carriers have polarisation efficiencies which are at least 6 times, and up to 300 times, smaller than those predicted for grain-related carriers.Comment: 6 pages + 13 pages online material, submitted to A&