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  1. Article ; Online: The Transporter-Mediated Cellular Uptake and Efflux of Pharmaceutical Drugs and Biotechnology Products

    Douglas B. Kell

    Molecules, Vol 26, Iss 5629, p

    How and Why Phospholipid Bilayer Transport Is Negligible in Real Biomembranes

    2021  Volume 5629

    Abstract: Over the years, my colleagues and I have come to realise that the likelihood of pharmaceutical drugs being able to diffuse through whatever unhindered phospholipid bilayer may exist in intact biological membranes in vivo is vanishingly low. This is ... ...

    Abstract Over the years, my colleagues and I have come to realise that the likelihood of pharmaceutical drugs being able to diffuse through whatever unhindered phospholipid bilayer may exist in intact biological membranes in vivo is vanishingly low. This is because (i) most real biomembranes are mostly protein, not lipid, (ii) unlike purely lipid bilayers that can form transient aqueous channels, the high concentrations of proteins serve to stop such activity, (iii) natural evolution long ago selected against transport methods that just let any undesirable products enter a cell, (iv) transporters have now been identified for all kinds of molecules (even water) that were once thought not to require them, (v) many experiments show a massive variation in the uptake of drugs between different cells, tissues, and organisms, that cannot be explained if lipid bilayer transport is significant or if efflux were the only differentiator, and (vi) many experiments that manipulate the expression level of individual transporters as an independent variable demonstrate their role in drug and nutrient uptake (including in cytotoxicity or adverse drug reactions). This makes such transporters valuable both as a means of targeting drugs (not least anti-infectives) to selected cells or tissues and also as drug targets. The same considerations apply to the exploitation of substrate uptake and product efflux transporters in biotechnology. We are also beginning to recognise that transporters are more promiscuous, and antiporter activity is much more widespread, than had been realised, and that such processes are adaptive (i.e., were selected by natural evolution). The purpose of the present review is to summarise the above, and to rehearse and update readers on recent developments. These developments lead us to retain and indeed to strengthen our contention that for transmembrane pharmaceutical drug transport “phospholipid bilayer transport is negligible”.
    Keywords membrane transport ; pharmaceuticals ; drugs ; energy coupling ; biotechnology ; ADME ; Organic chemistry ; QD241-441
    Subject code 612
    Language English
    Publishing date 2021-09-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: FragNet, a Contrastive Learning-Based Transformer Model for Clustering, Interpreting, Visualizing, and Navigating Chemical Space

    Aditya Divyakant Shrivastava / Douglas B. Kell

    Molecules, Vol 26, Iss 2065, p

    2021  Volume 2065

    Abstract: The question of molecular similarity is core in cheminformatics and is usually assessed via a pairwise comparison based on vectors of properties or molecular fingerprints. We recently exploited variational autoencoders to embed 6M molecules in a chemical ...

    Abstract The question of molecular similarity is core in cheminformatics and is usually assessed via a pairwise comparison based on vectors of properties or molecular fingerprints. We recently exploited variational autoencoders to embed 6M molecules in a chemical space, such that their (Euclidean) distance within the latent space so formed could be assessed within the framework of the entire molecular set. However, the standard objective function used did not seek to manipulate the latent space so as to cluster the molecules based on any perceived similarity. Using a set of some 160,000 molecules of biological relevance, we here bring together three modern elements of deep learning to create a novel and disentangled latent space, viz transformers, contrastive learning, and an embedded autoencoder. The effective dimensionality of the latent space was varied such that clear separation of individual types of molecules could be observed within individual dimensions of the latent space. The capacity of the network was such that many dimensions were not populated at all. As before, we assessed the utility of the representation by comparing clozapine with its near neighbors, and we also did the same for various antibiotics related to flucloxacillin. Transformers, especially when as here coupled with contrastive learning, effectively provide one-shot learning and lead to a successful and disentangled representation of molecular latent spaces that at once uses the entire training set in their construction while allowing “similar” molecules to cluster together in an effective and interpretable way.
    Keywords deep learning ; artificial intelligence ; generative methods ; chemical space ; neural networks ; transformers ; Organic chemistry ; QD241-441
    Subject code 006
    Language English
    Publishing date 2021-04-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Accelerating discovery

    Simone Turner / Gert Jacobus Laubscher / M Asad Khan / Douglas B. Kell / Etheresia Pretorius

    Heliyon, Vol 9, Iss 9, Pp e19605- (2023)

    A novel flow cytometric method for detecting fibrin(ogen) amyloid microclots using long COVID as a model

    2023  

    Abstract: Long COVID has become a significant global health and economic burden, yet there are currently no established methods or diagnostic tools to identify which patients might benefit from specific treatments. One of the major pathophysiological factors ... ...

    Abstract Long COVID has become a significant global health and economic burden, yet there are currently no established methods or diagnostic tools to identify which patients might benefit from specific treatments. One of the major pathophysiological factors contributing to Long COVID is the presence of hypercoagulability; this results in insoluble amyloid microclots that are resistant to fibrinolysis. Our previous research using fluorescence microscopy has demonstrated a significant amyloid microclot load in Long COVID patients. However, this approach lacked the elements of statistical robustness, objectivity, and rapid throughput. In the current study, we have used imaging flow cytometry for the first time to show a significantly increased concentration and size of these microclots. We identified notable variations in size and fluorescence between microclots in Long COVID and those of controls even using a 20× objective. By combining cell imaging and the high-event-rate and full-sample analysis nature of a conventional flow cytometer, imaging flow cytometry can eliminate erroneous results and increase accuracy in gating and analysis beyond what pure quantitative measurements from conventional flow cytometry can provide. Although imaging flow cytometry was used in our study, our results suggest that the signals indicating the presence of microclots should be easily detectable using a conventional flow cytometer. Flow cytometry is a more widely available technique than fluorescence microscopy and has been used in pathology laboratories for decades, rendering it a potentially more suitable and accessible method for detecting microclots in individuals suffering from Long COVID or conditions with similar pathology, such as myalgic encephalomyelitis.
    Keywords Long COVID ; Amyloid microclots ; Imaging flow cytometry ; Fluorescence ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
    Subject code 610
    Language English
    Publishing date 2023-09-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: The Biology of Lactoferrin, an Iron-Binding Protein That Can Help Defend Against Viruses and Bacteria

    Douglas B. Kell / Eugene L. Heyden / Etheresia Pretorius

    Frontiers in Immunology, Vol

    2020  Volume 11

    Abstract: Lactoferrin is a nutrient classically found in mammalian milk. It binds iron and is transferred via a variety of receptors into and between cells, serum, bile, and cerebrospinal fluid. It has important immunological properties, and is both antibacterial ... ...

    Abstract Lactoferrin is a nutrient classically found in mammalian milk. It binds iron and is transferred via a variety of receptors into and between cells, serum, bile, and cerebrospinal fluid. It has important immunological properties, and is both antibacterial and antiviral. In particular, there is evidence that it can bind to at least some of the receptors used by coronaviruses and thereby block their entry. Of importance are Heparan Sulfate Proteoglycans (HSPGs) and the host receptor angiotensin-converting enzyme 2 (ACE2), as based on other activities lactoferrin might prevent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from attaching to the host cells. Lactoferrin (and more specifically enteric-coated LF because of increased bioavailability) may consequently be of preventive and therapeutic value during the present COVID-19 pandemic.
    Keywords lactoferrin ; coronaviruses ; iron ; membrane receptors ; HSPGs ; Immunologic diseases. Allergy ; RC581-607 ; covid19
    Subject code 572
    Language English
    Publishing date 2020-05-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Structural Similarities between Some Common Fluorophores Used in Biology, Marketed Drugs, Endogenous Metabolites, and Natural Products

    Steve O’Hagan / Douglas B. Kell

    Marine Drugs, Vol 18, Iss 582, p

    2020  Volume 582

    Abstract: It is known that at least some fluorophores can act as ‘surrogate’ substrates for solute carriers (SLCs) involved in pharmaceutical drug uptake, and this promiscuity is taken to reflect at least a certain structural similarity. As part of a comprehensive ...

    Abstract It is known that at least some fluorophores can act as ‘surrogate’ substrates for solute carriers (SLCs) involved in pharmaceutical drug uptake, and this promiscuity is taken to reflect at least a certain structural similarity. As part of a comprehensive study seeking the ‘natural’ substrates of ‘orphan’ transporters that also serve to take up pharmaceutical drugs into cells, we have noted that many drugs bear structural similarities to natural products. A cursory inspection of common fluorophores indicates that they too are surprisingly ‘drug-like’, and they also enter at least some cells. Some are also known to be substrates of efflux transporters. Consequently, we sought to assess the structural similarity of common fluorophores to marketed drugs, endogenous mammalian metabolites, and natural products. We used a set of some 150 fluorophores along with standard fingerprinting methods and the Tanimoto similarity metric. Results: The great majority of fluorophores tested exhibited significant similarity (Tanimoto similarity > 0.75) to at least one drug, as judged via descriptor properties (especially their aromaticity, for identifiable reasons that we explain), by molecular fingerprints, by visual inspection, and via the “quantitative estimate of drug likeness” technique. It is concluded that this set of fluorophores does overlap with a significant part of both the drug space and natural products space. Consequently, fluorophores do indeed offer a much wider opportunity than had possibly been realised to be used as surrogate uptake molecules in the competitive or trans-stimulation assay of membrane transporter activities.
    Keywords drugs ; natural products ; fluorophores ; fingerprinting ; similarity ; cheminformatics ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2020-11-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: The transporter-mediated cellular uptake of pharmaceutical drugs is based on their metabolite-likeness and not on their bulk biophysical properties

    Douglas B. Kell

    Perspectives in Science, Vol 6, Iss C, Pp 66-

    Towards a systems pharmacology

    2015  Volume 83

    Abstract: Several recent developments are brought together: (i) the new availability of a consensus, curated human metabolic network reconstruction (Recon2), approximately a third of whose steps are represented by transporters, (ii) the recognition that most ... ...

    Abstract Several recent developments are brought together: (i) the new availability of a consensus, curated human metabolic network reconstruction (Recon2), approximately a third of whose steps are represented by transporters, (ii) the recognition that most successful (marketed) drugs, as well as natural products, bear significant similarities to the metabolites in Recon2, (iii) the recognition that to get into and out of cells such drugs hitchhike on the transporters that are part of normal intermediary metabolism, and the consequent recognition that for intact biomembrane Phospholipid Bilayer diffusion Is Negligible (PBIN), and (iv) the consequent recognition that we need to exploit this and to use more phenotypic assays to understand how drugs affect cells and organisms. I show in particular that lipophilicity is a very poor predictor of drug permeability, and that we need to (and can) bring together our knowledge of both pharmacology and systems biology modelling into a new systems pharmacology.
    Keywords Drug transporters ; Biophysics ; Recon2 ; Narcotics ; General anaesthetics ; Permeability ; Systems pharmacology ; Science ; Q ; Science (General) ; Q1-390
    Subject code 004
    Language English
    Publishing date 2015-12-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: The Occurrence of Hyperactivated Platelets and Fibrinaloid Microclots in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)

    Jean M. Nunes / Arneaux Kruger / Amy Proal / Douglas B. Kell / Etheresia Pretorius

    Pharmaceuticals, Vol 15, Iss 8, p

    2022  Volume 931

    Abstract: We have previously demonstrated that platelet-poor plasma (PPP) obtained from patients with Long COVID/Post-Acute Sequelae of COVID-19 (PASC) is characterized by a hypercoagulable state and contains hyperactivated platelets and considerable numbers of ... ...

    Abstract We have previously demonstrated that platelet-poor plasma (PPP) obtained from patients with Long COVID/Post-Acute Sequelae of COVID-19 (PASC) is characterized by a hypercoagulable state and contains hyperactivated platelets and considerable numbers of already-formed amyloid fibrin(ogen) or fibrinaloid microclots. Due to the substantial overlap in symptoms and etiology between Long COVID/PASC and ME/CFS, we investigated whether coagulopathies reflected in Long COVID/PASC—hypercoagulability, platelet hyperactivation, and fibrinaloid microclot formation—were present in individuals with ME/CFS and gender- and age-matched healthy controls. ME/CFS samples showed significant hypercoagulability as judged by thromboelastography of both whole blood and platelet-poor plasma. The area of plasma images containing fibrinaloid microclots was commonly more than 10-fold greater in untreated PPP from individuals with ME/CFS than in that of healthy controls. A similar difference was found when the plasma samples were treated with thrombin. Using fluorescently labelled PAC-1, which recognizes glycoprotein IIb/IIIa, and CD62P, which binds P-selectin, we observed hyperactivation of platelets in ME/CFS hematocrit samples. Using a quantitative scoring system, the ME/CFS platelets were found to have a mean spreading score of 2.72 ± 1.24 vs. 1.00 (activation with pseudopodia formation) for healthy controls. We conclude that ME/CFS is accompanied by substantial and measurable changes in coagulability, platelet hyperactivation, and fibrinaloid microclot formation. However, the fibrinaloid microclot load was not as great as was previously noted in Long COVID/PASC. Fibrinaloid microclots, in particular, may contribute to many ME/CFS symptoms, such as fatigue, seen in patients with ME/CFS, via the (temporary) blockage of microcapillaries and hence ischemia. Furthermore, fibrinaloid microclots might damage the endothelium. The discovery of these biomarkers represents an important development in ME/CFS research. It also points to possible uses ...
    Keywords myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) ; platelets ; fibrinaloid microclots ; hypercoagulability ; Medicine ; R ; Pharmacy and materia medica ; RS1-441
    Subject code 630
    Language English
    Publishing date 2022-07-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Data sharing

    Sunday O. Oladejo / Liam R. Watson / Bruce W. Watson / Kanshukan Rajaratnam / Maritha J. Kotze / Douglas B. Kell / Etheresia Pretorius

    South African Journal of Science, Vol 119, Iss 5/

    A Long COVID perspective, challenges, and road map for the future

    2023  Volume 6

    Abstract: Long COVID’ is the term used to describe the phenomenon in which patients who have survived a COVID-19 infection continue to experience prolonged SARS-CoV-2 symptoms. Millions of people across the globe are affected by Long COVID. Solving the Long COVID ...

    Abstract ‘Long COVID’ is the term used to describe the phenomenon in which patients who have survived a COVID-19 infection continue to experience prolonged SARS-CoV-2 symptoms. Millions of people across the globe are affected by Long COVID. Solving the Long COVID conundrum will require drawing upon the lessons of the COVID-19 pandemic, during which thousands of experts across diverse disciplines such as epidemiology, genomics, medicine, data science, and computer science collaborated, sharing data and pooling resources to attack the problem from multiple angles. Thus far, there has been no global consensus on the definition, diagnosis, and most effective treatment of Long COVID. In this work, we examine the possible applications of data sharing and data science in general with a view to, ultimately, understand Long COVID in greater detail and hasten relief for the millions of people experiencing it. We examine the literature and investigate the current state, challenges, and opportunities of data sharing in Long COVID research. Significance: Although millions of people across the globe have been diagnosed with Long COVID, there still exist many research gaps in our understanding of the condition and its underlying causes. This work aims to elevate the discussion surrounding data sharing and data science in the research community and to engage data sharing as an enabler to fast-track the process of finding effective treatment for Long COVID.
    Keywords Long COVID ; data sharing ; data science ; Science ; Q ; Science (General) ; Q1-390 ; Social Sciences ; H ; Social sciences (General) ; H1-99
    Subject code 306
    Language English
    Publishing date 2023-05-01T00:00:00Z
    Publisher Academy of Science of South Africa
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: TEG ® , Microclot and Platelet Mapping for Guiding Early Management of Severe COVID-19 Coagulopathy

    Gert Jacobus Laubscher / Petrus Johannes Lourens / Chantelle Venter / Douglas B Kell / Etheresia Pretorius

    Journal of Clinical Medicine, Vol 10, Iss 5381, p

    2021  Volume 5381

    Abstract: An important component of severe COVID-19 disease is virus-induced endothelilitis. This leads to disruption of normal endothelial function, initiating a state of failing normal clotting physiology. Massively increased levels of von Willebrand Factor (VWF) ...

    Abstract An important component of severe COVID-19 disease is virus-induced endothelilitis. This leads to disruption of normal endothelial function, initiating a state of failing normal clotting physiology. Massively increased levels of von Willebrand Factor (VWF) lead to overwhelming platelet activation, as well as activation of the enzymatic (intrinsic) clotting pathway. In addition, there is an impaired fibrinolysis, caused by, amongst others, increased levels of alpha-(2) antiplasmin. The end result is hypercoagulation (proven by thromboelastography ® (TEG ® )) and reduced fibrinolysis, inevitably leading to a difficult-to-overcome hypercoagulated physiological state. Platelets in circulation also plays a significant role in clot formation, but they themselves may also drive hypercoagulation when they are overactivated due to the interactions of their receptors with the endothelium, immune cells or circulating inflammatory molecules. From the literature it is clear that the role of platelets in severely ill COVID-19 patients has been markedly underestimated or even ignored. We here highlight the value of early management of severe COVID-19 coagulopathy as guided by TEG ® , microclot and platelet mapping. We also argue that the failure of clinical trials, where the efficacy of prophylactic versus therapeutic clexane (low molecular weight heparin (LMWH)) were not always successful, which may be because the significant role of platelet activation was not taken into account during the planning of the trial. We conclude that, because of the overwhelming alteration of clotting, the outcome of any trial evaluating an any single anticoagulant, including thrombolytic, would be negative. Here we suggest the use of the degree of platelet dysfunction and presence of microclots in circulation, together with TEG ® , might be used as a guideline for disease severity. A multi-pronged approach, guided by TEG ® and platelet mapping, would be required to maintain normal clotting physiology in severe COVID-19 disease.
    Keywords COVID-19 ; consumptive coagulopathy ; platelets ; blood clotting ; fibrinolysis ; von Willebrand factor ; Medicine ; R
    Subject code 333
    Language English
    Publishing date 2021-11-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Immunological Tolerance, Pregnancy, and Preeclampsia

    Louise C. Kenny / Douglas B. Kell

    Frontiers in Medicine, Vol

    The Roles of Semen Microbes and the Father†

    2018  Volume 4

    Abstract: Although it is widely considered, in many cases, to involve two separable stages (poor placentation followed by oxidative stress/inflammation), the precise originating causes of preeclampsia (PE) remain elusive. We have previously brought together some ... ...

    Abstract Although it is widely considered, in many cases, to involve two separable stages (poor placentation followed by oxidative stress/inflammation), the precise originating causes of preeclampsia (PE) remain elusive. We have previously brought together some of the considerable evidence that a (dormant) microbial component is commonly a significant part of its etiology. However, apart from recognizing, consistent with this view, that the many inflammatory markers of PE are also increased in infection, we had little to say about immunity, whether innate or adaptive. In addition, we focused on the gut, oral and female urinary tract microbiomes as the main sources of the infection. We here marshall further evidence for an infectious component in PE, focusing on the immunological tolerance characteristic of pregnancy, and the well-established fact that increased exposure to the father’s semen assists this immunological tolerance. As well as these benefits, however, semen is not sterile, microbial tolerance mechanisms may exist, and we also review the evidence that semen may be responsible for inoculating the developing conceptus (and maybe the placenta) with microbes, not all of which are benign. It is suggested that when they are not, this may be a significant cause of PE. A variety of epidemiological and other evidence is entirely consistent with this, not least correlations between semen infection, infertility and PE. Our view also leads to a series of other, testable predictions. Overall, we argue for a significant paternal role in the development of PE through microbial infection of the mother via insemination.
    Keywords preeclampsia ; immunology ; microbes ; dormancy ; semen ; infection ; Medicine (General) ; R5-920
    Subject code 630
    Language English
    Publishing date 2018-01-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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