Biochemistry and Pharmacology - Research Publications

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    Bioinformatics Approaches to Predict Mutation Effects in the Binding Site of the Proangiogenic Molecule CD93.
    Cicaloni, V ; Karmakar, M ; Frusciante, L ; Pettini, F ; Visibelli, A ; Orlandini, M ; Galvagni, F ; Mongiat, M ; Silk, M ; Nardi, F ; Ascher, D ; Santucci, A ; Spiga, O (Frontiers Media SA, 2022)
    The transmembrane glycoprotein CD93 has been identified as a potential new target to inhibit tumor angiogenesis. Recently, Multimerin-2 (MMRN2), a pan-endothelial extracellular matrix protein, has been identified as a ligand for CD93, but the interaction mechanism between these two proteins is yet to be studied. In this article, we aim to investigate the structural and functional effects of induced mutations on the binding domain of CD93 to MMRN2. Starting from experimental data, we assessed how specific mutations in the C-type lectin-like domain (CTLD) affect the binding interaction profile. We described a four-step workflow in order to predict the effects of variations on the inter-residue interaction network at the PPI, based on evolutionary information, complex network metrics, and energetic affinity. We showed that the application of computational approaches, combined with experimental data, allowed us to gain more in-depth molecular insights into the CD93-MMRN2 interaction, offering a platform for developing innovative therapeutics able to target these molecules and block their interaction. This comprehensive molecular insight might prove useful in drug design in cancer therapy.
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    Sequence grammar underlying the unfolding and phase separation of globular proteins
    Ruff, KM ; Choi, YH ; Cox, D ; Ormsby, AR ; Myung, Y ; Ascher, DB ; Radford, SE ; V. Pappu, R ; Hatters, DM (CELL PRESS, 2022-09-01)
    Aberrant phase separation of globular proteins is associated with many diseases. Here, we use a model protein system to understand how the unfolded states of globular proteins drive phase separation and the formation of unfolded protein deposits (UPODs). We find that for UPODs to form, the concentrations of unfolded molecules must be above a threshold value. Additionally, unfolded molecules must possess appropriate sequence grammars to drive phase separation. While UPODs recruit molecular chaperones, their compositional profiles are also influenced by synergistic physicochemical interactions governed by the sequence grammars of unfolded proteins and cellular proteins. Overall, the driving forces for phase separation and the compositional profiles of UPODs are governed by the sequence grammars of unfolded proteins. Our studies highlight the need for uncovering the sequence grammars of unfolded proteins that drive UPOD formation and cause gain-of-function interactions whereby proteins are aberrantly recruited into UPODs.
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    Structural landscapes of PPI interfaces
    Rodrigues, CHM ; Pires, DE ; Blundell, TL ; Ascher, DB (OXFORD UNIV PRESS, 2022-06-02)
    Proteins are capable of highly specific interactions and are responsible for a wide range of functions, making them attractive in the pursuit of new therapeutic options. Previous studies focusing on overall geometry of protein-protein interfaces, however, concluded that PPI interfaces were generally flat. More recently, this idea has been challenged by their structural and thermodynamic characterisation, suggesting the existence of concave binding sites that are closer in character to traditional small-molecule binding sites, rather than exhibiting complete flatness. Here, we present a large-scale analysis of binding geometry and physicochemical properties of all protein-protein interfaces available in the Protein Data Bank. In this review, we provide a comprehensive overview of the protein-protein interface landscape, including evidence that even for overall larger, more flat interfaces that utilize discontinuous interacting regions, small and potentially druggable pockets are utilized at binding sites.
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    Understanding and predicting the functional consequences of missense mutations in BRCA1 and BRCA2.
    Aljarf, R ; Shen, M ; Pires, DEV ; Ascher, DB (Springer Science and Business Media LLC, 2022-06-21)
    BRCA1 and BRCA2 are tumour suppressor genes that play a critical role in maintaining genomic stability via the DNA repair mechanism. DNA repair defects caused by BRCA1 and BRCA2 missense variants increase the risk of developing breast and ovarian cancers. Accurate identification of these variants becomes clinically relevant, as means to guide personalized patient management and early detection. Next-generation sequencing efforts have significantly increased data availability but also the discovery of variants of uncertain significance that need interpretation. Experimental approaches used to measure the molecular consequences of these variants, however, are usually costly and time-consuming. Therefore, computational tools have emerged as faster alternatives for assisting in the interpretation of the clinical significance of newly discovered variants. To better understand and predict variant pathogenicity in BRCA1 and BRCA2, various machine learning algorithms have been proposed, however presented limited performance. Here we present BRCA1 and BRCA2 gene-specific models and a generic model for quantifying the functional impacts of single-point missense variants in these genes. Across tenfold cross-validation, our final models achieved a Matthew's Correlation Coefficient (MCC) of up to 0.98 and comparable performance of up to 0.89 across independent, non-redundant blind tests, outperforming alternative approaches. We believe our predictive tool will be a valuable resource for providing insights into understanding and interpreting the functional consequences of missense variants in these genes and as a tool for guiding the interpretation of newly discovered variants and prioritizing mutations for experimental validation.
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    Evaluating hierarchical machine learning approaches to classify biological databases
    Rezende, PM ; Xavier, JS ; Ascher, DB ; Fernandes, GR ; Pires, DE (OXFORD UNIV PRESS, 2022-06-21)
    The rate of biological data generation has increased dramatically in recent years, which has driven the importance of databases as a resource to guide innovation and the generation of biological insights. Given the complexity and scale of these databases, automatic data classification is often required. Biological data sets are often hierarchical in nature, with varying degrees of complexity, imposing different challenges to train, test and validate accurate and generalizable classification models. While some approaches to classify hierarchical data have been proposed, no guidelines regarding their utility, applicability and limitations have been explored or implemented. These include 'Local' approaches considering the hierarchy, building models per level or node, and 'Global' hierarchical classification, using a flat classification approach. To fill this gap, here we have systematically contrasted the performance of 'Local per Level' and 'Local per Node' approaches with a 'Global' approach applied to two different hierarchical datasets: BioLip and CATH. The results show how different components of hierarchical data sets, such as variation coefficient and prediction by depth, can guide the choice of appropriate classification schemes. Finally, we provide guidelines to support this process when embarking on a hierarchical classification task, which will help optimize computational resources and predictive performance.
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    Germline variants in tumor suppressor FBXW7 lead to impaired ubiquitination and a neurodevelopmental syndrome
    Stephenson, SEM ; Costain, G ; Blok, LER ; Silk, MA ; Nguyen, TB ; Dong, X ; Alhuzaimi, DE ; Dowling, JJ ; Walker, S ; Amburgey, K ; Hayeems, RZ ; Rodan, LH ; Schwartz, MA ; Picker, J ; Lynch, SA ; Gupta, A ; Rasmussen, KJ ; Schimmenti, LA ; Klee, EW ; Niu, Z ; Agre, KE ; Chilton, I ; Chung, WK ; Revah-Politi, A ; Au, PYB ; Griffith, C ; Racobaldo, M ; Raas-Rothschild, A ; Ben Zeev, B ; Barel, O ; Moutton, S ; Morice-Picard, F ; Carmignac, V ; Cornaton, J ; Marle, N ; Devinsky, O ; Stimach, C ; Wechsler, SB ; Hainline, BE ; Sapp, K ; Willems, M ; Bruel, A ; Dias, K-R ; Evans, C-A ; Roscioli, T ; Sachdev, R ; Temple, SEL ; Zhu, Y ; Baker, JJ ; Scheffer, IE ; Gardiner, FJ ; Schneider, AL ; Muir, AM ; Mefford, HC ; Crunk, A ; Heise, EM ; Millan, F ; Monaghan, KG ; Person, R ; Rhodes, L ; Richards, S ; Wentzensen, IM ; Cogne, B ; Isidor, B ; Nizon, M ; Vincent, M ; Besnard, T ; Piton, A ; Marcelis, C ; Kato, K ; Koyama, N ; Ogi, T ; Goh, ES-Y ; Richmond, C ; Amor, DJ ; Boyce, JO ; Morgan, AT ; Hildebrand, MS ; Kaspi, A ; Bahlo, M ; Fridriksdottir, R ; Katrinardottir, H ; Sulem, P ; Stefansson, K ; Bjornsson, HT ; Mandelstam, S ; Morleo, M ; Mariani, M ; Scala, M ; Accogli, A ; Torella, A ; Capra, V ; Wallis, M ; Jansen, S ; Waisfisz, Q ; de Haan, H ; Sadedin, S ; Lim, SC ; White, SM ; Ascher, DB ; Schenck, A ; Lockhart, PJ ; Christodoulou, J ; Tan, TY (CELL PRESS, 2022-04-07)
    Neurodevelopmental disorders are highly heterogenous conditions resulting from abnormalities of brain architecture and/or function. FBXW7 (F-box and WD-repeat-domain-containing 7), a recognized developmental regulator and tumor suppressor, has been shown to regulate cell-cycle progression and cell growth and survival by targeting substrates including CYCLIN E1/2 and NOTCH for degradation via the ubiquitin proteasome system. We used a genotype-first approach and global data-sharing platforms to identify 35 individuals harboring de novo and inherited FBXW7 germline monoallelic chromosomal deletions and nonsense, frameshift, splice-site, and missense variants associated with a neurodevelopmental syndrome. The FBXW7 neurodevelopmental syndrome is distinguished by global developmental delay, borderline to severe intellectual disability, hypotonia, and gastrointestinal issues. Brain imaging detailed variable underlying structural abnormalities affecting the cerebellum, corpus collosum, and white matter. A crystal-structure model of FBXW7 predicted that missense variants were clustered at the substrate-binding surface of the WD40 domain and that these might reduce FBXW7 substrate binding affinity. Expression of recombinant FBXW7 missense variants in cultured cells demonstrated impaired CYCLIN E1 and CYCLIN E2 turnover. Pan-neuronal knockdown of the Drosophila ortholog, archipelago, impaired learning and neuronal function. Collectively, the data presented herein provide compelling evidence of an F-Box protein-related, phenotypically variable neurodevelopmental disorder associated with monoallelic variants in FBXW7.
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    CSM-peptides: A computational approach to rapid identification of therapeutic peptides
    Rodrigues, CHM ; Garg, A ; Keizer, D ; Pires, DE ; Ascher, DB (WILEY, 2022-10-01)
    Peptides are attractive alternatives for the development of new therapeutic strategies due to their versatility and low complexity of synthesis. Increasing interest in these molecules has led to the creation of large collections of experimentally characterized therapeutic peptides, which greatly contributes to development of data-driven computational approaches. Here we propose CSM-peptides, a novel machine learning method for rapid identification of eight different types of therapeutic peptides: anti-angiogenic, anti-bacterial, anti-cancer, anti-inflammatory, anti-viral, cell-penetrating, quorum sensing, and surface binding. Our method has shown to outperform existing approaches, achieving an AUC of up to 0.92 on independent blind tests, and consistent performance on cross-validation. We anticipate CSM-peptides to be of great value in helping screening large libraries to identify novel peptides with therapeutic potential and have made it freely available as a user-friendly web server and Application Programming Interface at https://biosig.lab.uq.edu.au/csm_peptides.
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    CSM-Potential: mapping protein interactions and biological ligands in 3D space using geometric deep learning
    Rodrigues, CHM ; Ascher, DB (OXFORD UNIV PRESS, 2022-05-24)
    Recent advances in protein structural modelling have enabled the accurate prediction of the holo 3D structures of almost any protein, however protein function is intrinsically linked to the interactions it makes. While a number of computational approaches have been proposed to explore potential biological interactions, they have been limited to specific interactions, and have not been readily accessible for non-experts or use in bioinformatics pipelines. Here we present CSM-Potential, a geometric deep learning approach to identify regions of a protein surface that are likely to mediate protein-protein and protein-ligand interactions in order to provide a link between 3D structure and biological function. Our method has shown robust performance, outperforming existing methods for both predictive tasks. By assessing the performance of CSM-Potential on independent blind tests, we show that our method was able to achieve ROC AUC values of up to 0.81 for the identification of potential protein-protein binding sites, and up to 0.96 accuracy on biological ligand classification. Our method is freely available as a user-friendly and easy-to-use web server and API at http://biosig.unimelb.edu.au/csm_potential.
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    cropCSM: designing safe and potent herbicides with graph-based signatures
    Pires, DE ; Stubbs, KA ; Mylne, JS ; Ascher, DB (OXFORD UNIV PRESS, 2022-02-24)
    Herbicides have revolutionised weed management, increased crop yields and improved profitability allowing for an increase in worldwide food security. Their widespread use, however, has also led to a rise in resistance and concerns about their environmental impact. Despite the need for potent and safe herbicidal molecules, no herbicide with a new mode of action has reached the market in 30 years. Although development of computational approaches has proven invaluable to guide rational drug discovery pipelines, leading to higher hit rates and lower attrition due to poor toxicity, little has been done in contrast for herbicide design. To fill this gap, we have developed cropCSM, a computational platform to help identify new, potent, nontoxic and environmentally safe herbicides. By using a knowledge-based approach, we identified physicochemical properties and substructures enriched in safe herbicides. By representing the small molecules as a graph, we leveraged these insights to guide the development of predictive models trained and tested on the largest collected data set of molecules with experimentally characterised herbicidal profiles to date (over 4500 compounds). In addition, we developed six new environmental and human toxicity predictors, spanning five different species to assist in molecule prioritisation. cropCSM was able to correctly identify 97% of herbicides currently available commercially, while predicting toxicity profiles with accuracies of up to 92%. We believe cropCSM will be an essential tool for the enrichment of screening libraries and to guide the development of potent and safe herbicides. We have made the method freely available through a user-friendly webserver at http://biosig.unimelb.edu.au/crop_csm.
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    Systematic evaluation of computational tools to predict the effects of mutations on protein stability in the absence of experimental structures
    Pan, Q ; Nguyen, TB ; Ascher, DB ; Pires, DE (OXFORD UNIV PRESS, 2022-03-10)
    Changes in protein sequence can have dramatic effects on how proteins fold, their stability and dynamics. Over the last 20 years, pioneering methods have been developed to try to estimate the effects of missense mutations on protein stability, leveraging growing availability of protein 3D structures. These, however, have been developed and validated using experimentally derived structures and biophysical measurements. A large proportion of protein structures remain to be experimentally elucidated and, while many studies have based their conclusions on predictions made using homology models, there has been no systematic evaluation of the reliability of these tools in the absence of experimental structural data. We have, therefore, systematically investigated the performance and robustness of ten widely used structural methods when presented with homology models built using templates at a range of sequence identity levels (from 15% to 95%) and contrasted performance with sequence-based tools, as a baseline. We found there is indeed performance deterioration on homology models built using templates with sequence identity below 40%, where sequence-based tools might become preferable. This was most marked for mutations in solvent exposed residues and stabilizing mutations. As structure prediction tools improve, the reliability of these predictors is expected to follow, however we strongly suggest that these factors should be taken into consideration when interpreting results from structure-based predictors of mutation effects on protein stability.