Database of 4 Million Medicinal Chemistry-Relevant Ring Systems

Central ring systems are the most important part of bioactive molecules. They determine molecule shape, keep substituents in their proper positions, and also influence global molecular properties. In the present study, a database of 4 million medicinal chemistry-relevant ring systems has been created, not by crude random enumeration but by applying a set of rules derived by analyzing rings present in bioactive molecules. The aromatic properties and tautomer stability of generated rings have also been considered to ensure that the rings in the database are stable and chemically reasonable. 99.2% of these rings are novel and not included in molecules in the ChEMBL or PubChem databases. This large database of ring systems has been created with the goal to provide support for bioisosteric design and scaffold hopping as well as to be used in generative chemistry applications. The complete set of created rings is available for download in the SMILES format from https://peter-ertl.com/molecular/data/

MOESM1 of An algorithm to identify functional groups in organic molecules

Additional file 1. List of 768 functional group with their frequencies in pseudo-SMILES notation

Evaluation of a Semi-Automated Workflow for Fragment Growing

Intelligent Automatic Design (IADE) is an expert system developed at Novartis to identify nonclassical bioisosteres. In addition to bioisostere searching, one could also use IADE to grow a fragment bound to a protein. Here we report an evaluation of IADE as a tool for fragment growing. Three examples from the literature served as test cases. In all three cases, IADE generated close analogues of the published compounds and reproduced their crystallographic binding modes. This exercise validated the use of the IADE system for fragment growing. We have also gained experience in optimizing the performance of IADE for this type of application

Microfluidic Migration and Wound Healing Assay Based on Mechanically Induced Injuries of Defined and Highly Reproducible Areas

All cell migration and wound healing assays are based on the inherent ability of adherent cells to move into adjacent cell-free areas, thus providing information on cell culture viability, cellular mechanisms and multicellular movements. Despite their widespread use for toxicological screening, biomedical research and pharmaceutical studies, to date no satisfactory technological solutions are available for the automated, miniaturized and integrated induction of defined wound areas. To bridge this technological gap, we have developed a lab-on-a-chip capable of mechanically inducing circular cell-free areas within confluent cell layers. The microdevices were fabricated using off-stoichiometric thiol-ene-epoxy (OSTEMER) polymer resulting in hard-polymer devices that are robust, cost-effective and disposable. We show that the pneumatically controlled membrane deflection/compression method not only generates highly reproducible (RSD 4%) injuries but also allows for repeated wounding in microfluidic environments. Performance analysis demonstrated that applied surface coating remains intact even after multiple wounding, while cell debris is simultaneously removed using laminar flow conditions. Furthermore, only a few injured cells were found along the edge of the circular cell-free areas, thus allowing reliable and reproducible cell migration of a wide range of surface sensitive anchorage dependent cell types. Practical application is demonstrated by investigating healing progression and endothelial cell migration in the absence and presence of an inflammatory cytokine (TNF-α) and a well-known cell proliferation inhibitor (mitomycin-C)

Microfluidic Migration and Wound Healing Assay Based on Mechanically Induced Injuries of Defined and Highly Reproducible Areas

All cell migration and wound healing assays are based on the inherent ability of adherent cells to move into adjacent cell-free areas, thus providing information on cell culture viability, cellular mechanisms and multicellular movements. Despite their widespread use for toxicological screening, biomedical research and pharmaceutical studies, to date no satisfactory technological solutions are available for the automated, miniaturized and integrated induction of defined wound areas. To bridge this technological gap, we have developed a lab-on-a-chip capable of mechanically inducing circular cell-free areas within confluent cell layers. The microdevices were fabricated using off-stoichiometric thiol-ene-epoxy (OSTEMER) polymer resulting in hard-polymer devices that are robust, cost-effective and disposable. We show that the pneumatically controlled membrane deflection/compression method not only generates highly reproducible (RSD 4%) injuries but also allows for repeated wounding in microfluidic environments. Performance analysis demonstrated that applied surface coating remains intact even after multiple wounding, while cell debris is simultaneously removed using laminar flow conditions. Furthermore, only a few injured cells were found along the edge of the circular cell-free areas, thus allowing reliable and reproducible cell migration of a wide range of surface sensitive anchorage dependent cell types. Practical application is demonstrated by investigating healing progression and endothelial cell migration in the absence and presence of an inflammatory cytokine (TNF-α) and a well-known cell proliferation inhibitor (mitomycin-C)

Application of a Biomimetic Nanoparticle-Based Mock Virus to Determine SARS-CoV‑2 Neutralizing Antibody Levels in Blood Samples Using a Lateral Flow Assay

The presence of neutralizing antibodies against SARS-CoV-2 in blood, acquired through previous infection or vaccination, is known to prevent the (re)occurrence of outbreaks unless the virus mutates. Therefore, the measurement of neutralizing antibodies constitutes an indispensable tool in assessing an individual’s and a population’s immunity against SARS-CoV-2. For this reason, we have developed an innovative lateral flow assay (LFA) capable of detecting blood-derived neutralizing antibodies using a biomimetic SARS-CoV-2 mock virus system. Here, functionalized gold nanoparticles (AuNPs) featuring the trimeric spike (S) protein at its surface imitate the virus’s structure and are applied to monitor the presence and efficacy of neutralizing antibodies in blood samples. The detection principle relies on the interaction between mock virus and the immobilized angiotensin-converting enzyme 2 (ACE2) receptor, which is inhibited when neutralizing antibodies are present. To further enhance the sensitivity of our competitive assay and identify low titers of neutralizing antibodies, an additional mixing pad is embedded into the device to increase the interaction time between mock virus and neutralizing antibodies. The developed LFA is benchmarked against the WHO International Standard (21/338) and demonstrated reliable quantification of neutralizing antibodies that inhibit ACE2 binding events down to a detection limit of an antibody titer of 59 IU/mL. Additional validation using whole blood and plasma samples showed reproducible results and good comparability to a laboratory-based reference test, thus highlighting its applicability for point-of-care testing

Development of a Multifunctional Nanobiointerface Based on Self-Assembled Fusion-Protein rSbpA/ZZ for Blood Cell Enrichment and Phenotyping

We present a multifunctional nanobiointerface for blood cell capture and phenotyping applications that features both excellent antifouling properties and high antibody activity. Multifunctionality is accomplished by modifying polymeric materials using self-assembled S-layer fusion-protein rSbpA/ZZ to immobilize high density antibodies at the two protein A binding sites of the rSbpA/ZZ nanolattice structure. Controlled orientation and alignment of the antibodies reduced antibody consumption 100-fold and increased cell capture efficiency 4-fold over standard methodologies. Cell analysis in complex samples was made possible by the remarkable antifouling properties of the rSbpA domain, while at the same time reducing unspecific binding and forgoing tedious blocking procedures. An automated microfluidic in situ cell analysis platform for isolation and phenotyping of primary peripheral blood mononuclear cells was developed as practical application. Results obtained using our automated microfluidic cell analysis platform showed that the multifunctional nanobiointerface can discriminate among T helper and cytotoxic T cells, and thymocytes. Additionally, on-chip cell capture under flow conditions using a high affinity CD 3 selective nanobiointerface preferentially isolated cells with strong surface marker expression. This means that our dynamic microfluidic cell purification method allows the enrichment of 773 CD 8 positive cytotoxic T cells out of a total blood cell population of 7728 PBMCs, which is an increase in cell enrichment of 8-fold with a purity of 85%

Simultaneous Determination of Oxygen and pH Inside Microfluidic Devices Using Core–Shell Nanosensors

A powerful online analysis setup for the simultaneous detection of oxygen and pH is presented. It features core–shell nanosensors, which enable contactless and inexpensive read-out using adapted oxygen meters via modified dual lifetime referencing in the frequency domain (phase shift measurements). Lipophilic indicator dyes were incorporated into core–shell structured poly­(styrene-<i>block</i>-vinylpyrrolidone) nanoparticles (average diameter = 180 nm) yielding oxygen nanosensors and pH nanosensors by applying different preparation protocols. The oxygen indicator platinum­(II) meso-tetra­(4-fluorophenyl) tetrabenzoporphyrin (PtTPTBPF) was entrapped into the polystyrene core (oxygen nanosensors) and a pH sensitive BF₂-chelated tetraarylazadipyrromethene dye (aza-BODIPY) was incorporated into the polyvinylpyrrolidone shell (pH nanosensors). The brightness of the pH nanoparticles was increased by more than 3 times using a light harvesting system. The nanosensors have several advantages such as being excitable with red light, emitting in the near-infrared spectral region, showing a high stability in aqueous media even at high particle concentrations, high ionic strength, or high protein concentrations and are spectrally compatible with the used read-out device. The resolution for oxygen of the setup is 0.5–2.0 hPa (approximately 0.02–0.08 mg/L of dissolved oxygen) at low oxygen concentrations (<50 hPa) and 4–8 hPa (approximately 0.16–0.32 mg/L of dissolved oxygen) at ambient air oxygen concentrations (approximately 200 hPa at 980 mbar air pressure) at room temperature. The pH resolution is 0.03–0.1 pH units within the dynamic range (apparent p<i>K</i>_a 7.23 ± 1.0) of the nanosensors. The sensors were used for online monitoring of pH changes during the enzymatic transformation of Penicillin G to 6-aminopenicillanic acid catalyzed by Penicillin G acylase in miniaturized stirred batch reactors or continuous flow microreactors

Monitoring Dynamic Interactions of Tumor Cells with Tissue and Immune Cells in a Lab-on-a-Chip

A complementary cell analysis method has been developed to assess the dynamic interactions of tumor cells with resident tissue and immune cells using optical light scattering and impedance sensing to shed light on tumor cell behavior. The combination of electroanalytical and optical biosensing technologies integrated in a lab-on-a-chip allows for continuous, label-free, and noninvasive probing of dynamic cell-to-cell interactions between adherent and nonadherent cocultures, thus providing real-time insights into tumor cell responses under physiologically relevant conditions. While the study of adherent cocultures is important for the understanding and suppression of metastatic invasion, the analysis of tumor cell interactions with nonadherent immune cells plays a vital role in cancer immunotherapy research. For the first time, the direct cell-to-cell interactions of tumor cells with bead-activated primary T cells were continuously assessed using an effector cell to target a cell ratio of 10:1

Image_3_Every Breath You Take: Non-invasive Real-Time Oxygen Biosensing in Two- and Three-Dimensional Microfluidic Cell Models.TIFF

<p>Knowledge on the availability of dissolved oxygen inside microfluidic cell culture systems is vital for recreating physiological-relevant microenvironments and for providing reliable and reproducible measurement conditions. It is important to highlight that in vivo cells experience a diverse range of oxygen tensions depending on the resident tissue type, which can also be recreated in vitro using specialized cell culture instruments that regulate external oxygen concentrations. While cell-culture conditions can be readily adjusted using state-of-the-art incubators, the control of physiological-relevant microenvironments within the microfluidic chip, however, requires the integration of oxygen sensors. Although several sensing approaches have been reported to monitor oxygen levels in the presence of cell monolayers, oxygen demands of microfluidic three-dimensional (3D)-cell cultures and spatio-temporal variations of oxygen concentrations inside two-dimensional (2D) and 3D cell culture systems are still largely unknown. To gain a better understanding on available oxygen levels inside organ-on-a-chip systems, we have therefore developed two different microfluidic devices containing embedded sensor arrays to monitor local oxygen levels to investigate (i) oxygen consumption rates of 2D and 3D hydrogel-based cell cultures, (ii) the establishment of oxygen gradients within cell culture chambers, and (iii) influence of microfluidic material (e.g., gas tight vs. gas permeable), surface coatings, cell densities, and medium flow rate on the respiratory activities of four different cell types. We demonstrate how dynamic control of cyclic normoxic-hypoxic cell microenvironments can be readily accomplished using programmable flow profiles employing both gas-impermeable and gas-permeable microfluidic biochips.</p