Search

Additional file 8: Figure S6. DTIs through docking. Molecular docking performed via SwissDock for novel predicted DTIs. (a) deltaG for the first 10 groups of molecules clustered by conformers similarity. (b) Binding locations with the lowest deltaG and all groups of conformers.

Additional file 5: Figure S3. Networks of drug and protein similarities. Topological representation of the DDS and PPS networks and PCA of drugs and targets based on embedded vectors.

Additional file 1: Related work. Related methods from literature. Summary of different embedding and similarity based methods for DTI prediction.

Additional file 6: Figure S4. PCA plots. PCA of embedded vectors of proteins coloured according to protein type.

Additional file 4: Figure S2. Datasets and data splitting. Details of data types and data splitting in cross-validation.

Additional file 3: Figure S1. Data collection procedure. (a) Workflow to collect data from the ChEMBL database, (b) Scatter plot of the pChEMBL value of collected DTIs on a boxplot.

Additional file 9: Figure S7. Drug similarity heatmaps. Drug-drug similarity for drugs predicted to interact with (a) ADAM17 and (b) MMP14.

Additional file 7: Figure S5. ROC plots over the ten-fold five times cross-validation.

Additional file 2: Datasets. Details about datasets used in this study are provided.

The nuclear receptor (NR) superfamily is comprised of transcription factors that are ligand-activated in their majority and play a pivotal role in biological functions that are essential for life, such as metabolism and homeostasis. Following activation, they undertake the regulation of the transcription of their target genes with the help of co-regulator proteins, rendering them very promising pharmacological targets. In total, 59 NRs have been discovered in several species of the Animalia kingdom, 20 of which are still orphan receptors. The present study aimed to further enlighten the evolutionary scenario that reveals the association between members of the NR superfamily. An updated evolutionary analysis was performed for the NR protein superfamily with the aim of clustering all the NRs, and discovering conserved regions and motifs that play major roles in their signaling pathway; the mechanisms of action were also investigated. The findings of the present study demonstrate a clear separation of the NR family in three majors monophyletic branches, the steroid hormone-related, the thyroid hormone-related and the retinoid X receptor-related clusters, from which, through evolution, may correspond to three ancestral NRs that were differentiated from a common ancestral NR. Copyright © 2021 Papageorgiou L. et al.

Antibodies are proteins that are the first line of defense in the adaptive immune response of vertebrates. Thereby, they are involved in a multitude of biochemical mechanisms and clinical manifestations with significant medical interest, such as autoimmunity, the regulation of infection, and cancer. An emerging field in antibody science that is of huge medicinal interest is the development of novel antibody-interacting drugs. Such entities are the antibody-drug conjugates (ADCs), which are a new type of targeted therapy, which consist of an antibody linked to a payload drug. Overall, the underlying principle of ADCs is the discerning delivery of a drug to a target, hoping to increase the potency of the original drug. Drugena suite is a pioneering platform that employs state-of-the-art computational biology methods in the fight against neurodegenerative diseases using ADCs. Drugena encompasses an up-to-date structural database of specialized antibodies for neurological disorders and the NCI database with over 96 million entities for the in silico development of ADCs. The pipeline of the Drugena suite has been divided into several steps and modules that are closely related with a synergistic fashion under a user-friendly graphical user interface. © Springer Nature Switzerland AG 2020.

Neurodegenerative diseases lead to the death of nerve cells in the brain or the spinal cord. A wide range of diseases are included within the group of neurodegenerative disorders, with the most common ones being dementia, Alzheimer’s, and Parkinson’s diseases. Millions of older people are suffering from such pathologies. The global increase of life expectancy unavoidably leads to a consequent increase in the number of people who will be at some degree affected by neurodegenerative-related diseases. At this moment, there is no effective therapy or treatment that can reverse the loss of neurons. A growing number of studies highlight the value of the consumption of medical foods, and in particular olive oil, as one of the most important components of the Mediterranean diet. A diet based on extra virgin olive oil seems to contribute toward the lowering of risk of age-related pathologies due to high phenol concentration. The link of a polyphenol found in extra virgin olive oil, namely, tyrosol, with the protein tyrosinase, associated to Parkinson’s disease is underlined as a paradigm of affiliation between polyphenols and neurodegenerative disorders. © Springer Nature Switzerland AG 2020.

The prospective observational cohort study COMPASS-COVID-19 aimed to develop a risk assessment model for early identification of hospitalized COVID-19 patients at risk for worsening disease. Patients with confirmed COVID-19 (n = 430) hospitalized between March 18 and April 21, 2020 were divided in derivation (n = 310) and validation (n = 120) cohorts. Two groups became evident: (1) good prognosis group (G-group) with patients hospitalized at the conventional COVID-19 ward and (2) Worsening disease group (W-group) with patients admitted to the intensive care unit (ICU) from the emergency departments. The study end point was disease worsening (acute respiratory failure, shock, myocardial dysfunction, bacterial or viral coinfections, and acute kidney injury) requiring ICU admission. All patients were routinely evaluated for full blood count, prothrombin time, fibrinogen, D-dimers, antithrombin (AT), and protein C activity. Data from the first hospitalization day at the conventional ward or the ICU were analyzed. Cardiovascular risk factors and comorbidities were routinely registered. Obesity, hypertension, diabetes and male gender, increased fibrinogen and D-dimers, thrombocytopenia, AT deficiency, lymphopenia, and an International Society on Thrombosis and Haemostasis (ISTH) score for compensated disseminated intravascular coagulation score (cDIC-ISTH) ≥ 5 were significant risk factors for worsening disease. The COMPASS-COVID-19 score was derived from multivariate analyses and includes obesity, gender, hemoglobin, lymphocyte, and the cDIC-ISTH score (including platelet count, prothrombin time, D-dimers, AT, and protein C levels). The score has a very good discriminating capacity to stratify patients at high and low risk for worsening disease, with an area under the receiver operating characteristic curve value of 0.77, a sensitivity of 81%, and a specificity of 60%. Application of the COMPASS-COVID-19 score at the validation cohort showed 96% sensitivity. The COMPASS-COVID-19 score is an accurate clinical decision-making tool for an easy identification of COVID-19 patients being at high risk for disease worsening. © 2020 Georg Thieme Verlag. All rights reserved.

Pesticides are necessary to fight agricultural pests, yet they are often nonspecific, and their widespread use is a hazard to the environment and human health. The genomic era allows for new approaches to specifically target agricultural pests, based on analysis of their genome and their microbiome. We present such an approach, to combat Bactrocera oleae, a widespread pest whose impact is devastating on olive production. To date, there is no specific pesticide to control it. Herein, we propose a novel strategy to manage this pest via identifying novel pharmacological targets on the genome of its obligate endosymbiotic bacterium Candidatus Erwinia dacicola. Three genes were selected as pharmacological targets. The 3D models of the Helicase, Polymerase, and Protease-C gene products were designed and subsequently optimized by means of molecular dynamics simulations. Successively, a series of structure-based pharmacophore models were elucidated in an effort to pave the way for the efficient high-throughput virtual screening of libraries of low molecular weight compounds and thus the discovery of novel modulating agents. Our methodology provides the means to design, test, and identify highly specific pest control substances that minimize the impact of toxic chemicals on health, economy, and the environment. © Springer Nature Switzerland AG 2020.

Herein, we deploy an in silico pipeline of structural bioinformatics, thermodynamics, and molecular dynamics to investigate the role of cortisol in circadian rhythms, biorhythms, stress response, and even sleep disorders. Our study shows that high concentrations of cortisol intercalate in the minor groove of DNA. This phenomenon widens the adjacent major grooves and provides the Clock/Bmal1 complex with more space to dock and interact with DNA. Then, the strong charges of cortisol pull the alpha helices of the Clock/Bmal1 complex and bend it inward, thus establishing stronger interactions and prolonged signaling. Our results indicate that elevated cortisol levels play an important role in stress, inflammation, and sleep disorders as a result of prolonged and stronger dsDNA – Clock/Bmal1 interactions. © Springer Nature Switzerland AG 2020.

Notch family proteins play a key role in a variety of developmental processes by controlling cell fate decisions and operating in a great number of biological processes in several organ systems, such as hematopoiesis, somatogenesis, vasculogenesis, neurogenesis and homeostasis. The Notch signaling pathway is crucial for the majority of developmental programs and regulates multiple pathogenic processes. Notch family receptors’ activation has been largely related to its multiple effects in sustaining oncogenesis. The Notch signaling pathway constitutes an ancient and conserved mechanism for cell to cell communication. Much of what is known about Notch family proteins function comes from studies done in Caenorhabditis Elegans and Drosophila Melanogaster. Although, human Notch homologs had also been identified, the molecular mechanisms which modulate the Notch signaling pathway remained substantially unknown. In this study, an updated evolutionary analysis of the Notch family members among 603 different organisms of all kingdoms, from bacteria to humans, was performed in order to discover key regions that have been conserved throughout evolution and play a major role in the Notch signaling pathway. The major goal of this study is the presentation of a novel updated phylogenetic tree for the Notch family as a reliable phylogeny “map”, in order to correlate information of the closely related members and identify new possible pharmacological targets that can be used in pathogenic cases, including cancer. Copyright 2020 Vlachakis et al.

Antibody V domain clustering is of paramount importance to a repertoire of immunology-related areas. Although several approaches have been proposed for antibody clustering, still no consensus has been reached. Numerous attempts use information from genes, protein sequences, 3D structures, and 3D surfaces in an effort to elucidate unknown action mechanisms directly related to their function and to either link them directly to diseases or drive the discovery of new medicines, such as antibody drug conjugates (ADC). Herein, we describe a new V domain antibody clustering method based on the comparison of the interaction sites between each antibody and its antigen. A more specific clustering analysis of the antibody’s V domain was provided using deep learning and data mining techniques. The multidimensional information was extracted from the structural resolved antibodies when they were captured to interact with other proteins. The available 3D structures of protein antigen-antibody (Ag-Ab) interfaces contain information about how antibody V domains recognize antigens as well as about which amino acids are involved in the recognition. As such, the antibody surface holds information about antigens’ folding that reside with the Ab-Ag interface residues and how they interact. In order to gain insight into the nature of such interactions, we propose a new simple philosophy to transform the conserved framework (fragment regions, complementarity-determining regions) of antibody V domain in a binary form using structural features of antibody-antigen interactions, toward identifying new antibody signatures in V domain binding activity. Finally, an advanced three-level hybrid classification scheme has been set for clustering antibodies in subgroups, which can combine the information from the protein sequences, the three-dimensional structures, and specific “key patterns” of recognized interactions. The clusters provide multilevel information about antibodies and antibody-antigen complexes. © Springer Nature Switzerland AG 2020.

Venous thromboembolism (VTE) is a common complication in newly diagnosed symptomatic multiple myeloma (NDMM) patients. We explored cellular and plasma hypercoagulability in NDMM patients to identify relevant biomarkers that can be used in combination with clinical factors in the development of a risk assessment model (RAM) for VTE. Untreated patients (n = 144) with NDMM were prospectively enrolled, baseline biomarkers prior to anti-myeloma treatment and thromboprophylaxis initiation were obtained. These were compared against values in a group of healthy individuals with similar age and sex distribution. The primary study end point was symptomatic VTE occurrence. At 12-month follow-up cumulative VTE rate was 10.4%. NDMM patients showed biological signs of cellular and plasma hypercoagulability and endothelial cell activation. Procoagulant phospholipid clotting time (Procoagulant-PPL) was shorter, P-selectin levels lower and thrombin generation attenuated overall compared to healthy subjects. Longer Procoag-PPL ® , lower endogenous thrombin potential (ETP), and higher levels of tissue factor pathway inhibitor (TFPI) were associated with VTE occurrence. Multivariate analysis showed that Procoag-PPL ® and ETP were independent risk factors for VTE. We conclude that Procoag-PPL ® and ETP can be prospectively incorporated into a RAM for VTE in MM in combination with clinical and disease risk factors. © 2018, The Author(s).

Background/Aim: The aim of the present study was to examine the relation between understanding of emotions and cardiovascular related diseases, namely coronary heart disease, diabetes mellitus and obesity. The uniqueness of this study lies in the fact that it examined the relationship between the cardiovascular related diseases named above and the understanding of emotions in the context of Emotional Intelligence (EI). Patients and Methods: The study was conducted in 300 participants during a 3 year period. All participants completed a self-report questionnaire, assessing various aspects of EI, such as self-emotion appraisal, other emotion appraisal, emotion regulation and use of emotions. As hypothesized, coronary heart disease is a prognostic factor of regulation of emotions. Results: The present study is an attempt to examine the relation between emotional understanding and cardiovascular related diseases, namely coronary heart disease, diabetes mellitus and obesity. Establishing which diseases are independent risk factors for the understanding of emotions, could have a significant impact on emotional health, through the treatment of these cardiovascular related diseases. Emotions were studied within the theoretical context of Emotional Intelligence (EI), which affects people’s physical and mental health. Conclusion: The results of this study emphasize on the relationship of cardiovascular related diseases and psychological characteristics, such as anxiety and anger, being aspects of EI. Additionally, this work fills a gap in the relevant Greek literature, as a first attempt to examine the correlation of EI with cardiovascular related diseases. © 2018 Universidade Federal Rural do Semi-Arido. All Rights Reserved.

Understanding the genetic and molecular basis of the detoxifying mechanism in Chlamydomonas reinhardtii is an important goal towards the development of bioremediation tools for contaminated environments. Glutathione transferases (GSTs, EC 2.5.1.18) are phase II metabolic enzymes that play important role in the detoxification of xenobiotic compounds. GSTs have been characterized extensively in land plants and animals but no evidence has yet been reported for their presence in C. reinhardtii. A genome survey of C. reinhardtii revealed the presence of fifteen GST-like isoenzymes (CrGSTs). Comparison by multiple sequence alignment generated a dendrogram, revealing the phylogenetic relationships of CrGSTs with other well-characterized GST classes. Notably, we identified sequences that are most closely related to the sigma class enzymes which so far have only been found in animals. Two sigma class related isoenzymes (CrGST10 and CrGST7) were cloned, expressed in E. coli and their substrate specificity and kinetic properties were determined towards a range of different xenobiotic substrates. The structural and kinetic features of the enzymes were studied by molecular modelling and site-directed mutagenesis. The catalytic role of active-site residue Tyr7 and the roles of Trp99 in determining substrate specificity and thermostability were investigated. Analysis of GSTome in green algae provides an opportunity to shine light on the roles of GSTs in cellular detoxification mechanism as well as to develop new biotechnological and environmental applications. © 2016 Elsevier B.V.

Trypanosoma brucei brucei (TBB) belongs to the unicellular parasitic protozoa organisms, specifically to the Trypanosoma genus of the Trypanosomatidae class. A variety of different vertebrate species can be infected by TBB, including humans and animals. Under particular conditions, the TBB can be hosted by wild and domestic animals; therefore, an important reservoir of infection always remains available to transmit through tsetse flies. Although the TBB parasite is one of the leading causes of death in the most underdeveloped countries, to date there is neither vaccination available nor any drug against TBB infection. The subunit RPB1 of the TBB DNAdirected RNA polymerase II (DdRpII) constitutes an ideal target for the design of novel inhibitors, since it is instrumental role is vital for the parasite's survival, proliferation, and transmission. A major goal of the described study is to provide insights for novel anti-TBB agents via a state-of-the-art drug discovery approach of the TBB DdRpII RPB1. In an attempt to understand the function and action mechanisms of this parasite enzyme related to its molecular structure, an in-depth evolutionary study has been conducted in parallel to the in silico molecular designing of the 3D enzyme model, based on state-of-the-art comparative modelling and molecular dynamics techniques. Based on the evolutionary studies results nine new invariant, first-time reported, highly conserved regions have been identified within the DdRpII family enzymes. Consequently, those patches have been examined both at the sequence and structural level and have been evaluated in regard to their pharmacological targeting appropriateness. Finally, the pharmacophore elucidation study enabled us to virtually in silico screen hundreds of compounds and evaluate their interaction capabilities with the enzyme. It was found that a series of chlorine-rich set of compounds were the optimal inhibitors for the TBB DdRpII RPB1 enzyme. All-in-all, herein we present a series of new sites on the TBB DdRpII RPB1 of high pharmacological interest, alongside the construction of the 3D model of the enzyme and the suggestion of a new in silico pharmacophore model for fast screening of potential inhibiting agents. © 2017 Papageorgiou et al.