1
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de Azevedo WF, Quiroga R, Villarreal MA, da Silveira NJF, Bitencourt-Ferreira G, da Silva AD, Veit-Acosta M, Oliveira PR, Tutone M, Biziukova N, Poroikov V, Tarasova O, Baud S. SAnDReS 2.0: Development of machine-learning models to explore the scoring function space. J Comput Chem 2024. [PMID: 38900052 DOI: 10.1002/jcc.27449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/04/2024] [Accepted: 06/02/2024] [Indexed: 06/21/2024]
Abstract
Classical scoring functions may exhibit low accuracy in determining ligand binding affinity for proteins. The availability of both protein-ligand structures and affinity data make it possible to develop machine-learning models focused on specific protein systems with superior predictive performance. Here, we report a new methodology named SAnDReS that combines AutoDock Vina 1.2 with 54 regression methods available in Scikit-Learn to calculate binding affinity based on protein-ligand structures. This approach allows exploration of the scoring function space. SAnDReS generates machine-learning models based on crystal, docked, and AlphaFold-generated structures. As a proof of concept, we examine the performance of SAnDReS-generated models in three case studies. For all three cases, our models outperformed classical scoring functions. Also, SAnDReS-generated models showed predictive performance close to or better than other machine-learning models such as KDEEP, CSM-lig, and ΔVinaRF20. SAnDReS 2.0 is available to download at https://github.com/azevedolab/sandres.
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Affiliation(s)
| | - Rodrigo Quiroga
- Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), CONICET-Departamento de Química Teórica y Computacional, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba, Argentina
| | - Marcos Ariel Villarreal
- Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), CONICET-Departamento de Química Teórica y Computacional, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba, Argentina
| | | | | | - Amauri Duarte da Silva
- Programa de Pós-Graduação em Tecnologias da Informação e Gestão em Saúde, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil
| | | | | | - Marco Tutone
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, Palermo, Italy
| | | | | | | | - Stéphaine Baud
- Laboratoire SiRMa, UMR CNRS/URCA 7369, UFR Sciences Exactes et Naturelles, Université de Reims Champagne-Ardenne, CNRS, MEDYC, Reims, France
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2
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Velloso JPL, Kovacs AS, Pires DEV, Ascher DB. AI-driven GPCR analysis, engineering, and targeting. Curr Opin Pharmacol 2024; 74:102427. [PMID: 38219398 DOI: 10.1016/j.coph.2023.102427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 01/16/2024]
Abstract
This article investigates the role of recent advances in Artificial Intelligence (AI) to revolutionise the study of G protein-coupled receptors (GPCRs). AI has been applied to many areas of GPCR research, including the application of machine learning (ML) in GPCR classification, prediction of GPCR activation levels, modelling GPCR 3D structures and interactions, understanding G-protein selectivity, aiding elucidation of GPCRs structures, and drug design. Despite progress, challenges in predicting GPCR structures and addressing the complex nature of GPCRs remain, providing avenues for future research and development.
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Affiliation(s)
- João P L Velloso
- Structural Biology and Bioinformatics, Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, Victoria, Australia; Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia; Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Aaron S Kovacs
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Douglas E V Pires
- Structural Biology and Bioinformatics, Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, Victoria, Australia; Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia; Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; School of Computing and Information Systems, University of Melbourne, Melbourne, Victoria, Australia.
| | - David B Ascher
- Structural Biology and Bioinformatics, Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, Victoria, Australia; Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia; Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia.
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3
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Desai A, Mahajan V, Ramabhadran RO, Mukherjee R. Binding order of substrate and cofactor in sulfonamide monooxygenase during sulfa drug degradation: in silico studies. J Biomol Struct Dyn 2024:1-15. [PMID: 38263732 DOI: 10.1080/07391102.2024.2306495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 01/10/2024] [Indexed: 01/25/2024]
Abstract
For decades, sulfonamide antibiotics have been used across industries such as agriculture and animal husbandry. However, the use and inadvertent misuse of these antibiotics have resulted in the advent of sulfonamide-drug-resistant strains due to antibiotic pollution. Enzymatic bioremediation of antibiotics remains a potential emerging solution to combat antibiotic pollution. Here, we propose an enzymatic model for the degradation of sulfonamides by Microbacterium sp. We have employed a multi-pronged computational strategy involving - protein structure modelling, ligand docking and molecular dynamics simulations to decipher a plausible binding order for the enzymatic degradation of sulfonamides by the bacterial sulfonamide monooxygenase, SulX. Our results enable us to predict that this degradation is achieved through the sequential binding of the antibiotic sulfonamide followed by the reduced flavin cofactor FMNH2, thereby laying the computational foundation for further advancements in enzyme-mediated degradation of the antibiotic. We also provide a list of experiments which may be performed to verify and follow-up on our in-silico studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Amogh Desai
- Department of Biology, Indian Institute of Science Education and Research Tirupati, Tirupati, India
| | - Ved Mahajan
- Department of Chemistry, Indian Institute of Science Education and Research Tirupati, Tirupati, India
| | - Raghunath O Ramabhadran
- Department of Chemistry, Indian Institute of Science Education and Research Tirupati, Tirupati, India
| | - Raju Mukherjee
- Department of Biology, Indian Institute of Science Education and Research Tirupati, Tirupati, India
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4
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Abstract
The greatest challenge in drug discovery remains the high rate of attrition across the different phases of the process, which cost the industry billions of dollars every year. While all phases remain crucial to ensure pharmaceutical-level safety, quality, and efficacy of the end product, streamlining these efforts toward compounds with success potential is pivotal for a more efficient and cost-effective process. The use of artificial intelligence (AI) within the pharmaceutical industry aims at just this, and has applications in preclinical screening for biological activity, optimization of pharmacokinetic properties for improved drug formulation, early toxicity prediction which reduces attrition, and pre-emptively screening for genetic changes in the biological target to improve therapeutic longevity. Here, we present a series of in silico tools that address these applications in small molecule development and describe how they can be embedded within the current pharmaceutical development pipeline.
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Affiliation(s)
- Adam Serghini
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Stephanie Portelli
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia.
| | - David B Ascher
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia.
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.
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5
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Rodrigues CHM, Ascher DB. CSM-Potential2: A comprehensive deep learning platform for the analysis of protein interacting interfaces. Proteins 2023. [PMID: 37870486 DOI: 10.1002/prot.26615] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 10/24/2023]
Abstract
Proteins are molecular machinery that participate in virtually all essential biological functions within the cell, which are tightly related to their 3D structure. The importance of understanding protein structure-function relationship is highlighted by the exponential growth of experimental structures, which has been greatly expanded by recent breakthroughs in protein structure prediction, most notably RosettaFold, and AlphaFold2. These advances have prompted the development of several computational approaches that leverage these data sources to explore potential biological interactions. However, most methods are generally limited to analysis of single types of interactions, such as protein-protein or protein-ligand interactions, and their complexity limits the usability to expert users. Here we report CSM-Potential2, a deep learning platform for the analysis of binding interfaces on protein structures. In addition to prediction of protein-protein interactions binding sites and classification of biological ligands, our new platform incorporates prediction of interactions with nucleic acids at the residue level and allows for ligand transplantation based on sequence and structure similarity to experimentally determined structures. We anticipate our platform to be a valuable resource that provides easy access to a range of state-of-the-art methods to expert and non-expert users for the study of biological interactions. Our tool is freely available as an easy-to-use web server and API available at https://biosig.lab.uq.edu.au/csm_potential.
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Affiliation(s)
- Carlos H M Rodrigues
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - David B Ascher
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
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6
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PSnpBind-ML: predicting the effect of binding site mutations on protein-ligand binding affinity. J Cheminform 2023; 15:31. [PMID: 36864534 PMCID: PMC9983232 DOI: 10.1186/s13321-023-00701-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/17/2023] [Indexed: 03/04/2023] Open
Abstract
Protein mutations, especially those which occur in the binding site, play an important role in inter-individual drug response and may alter binding affinity and thus impact the drug's efficacy and side effects. Unfortunately, large-scale experimental screening of ligand-binding against protein variants is still time-consuming and expensive. Alternatively, in silico approaches can play a role in guiding those experiments. Methods ranging from computationally cheaper machine learning (ML) to the more expensive molecular dynamics have been applied to accurately predict the mutation effects. However, these effects have been mostly studied on limited and small datasets, while ideally a large dataset of binding affinity changes due to binding site mutations is needed. In this work, we used the PSnpBind database with six hundred thousand docking experiments to train a machine learning model predicting protein-ligand binding affinity for both wild-type proteins and their variants with a single-point mutation in the binding site. A numerical representation of the protein, binding site, mutation, and ligand information was encoded using 256 features, half of them were manually selected based on domain knowledge. A machine learning approach composed of two regression models is proposed, the first predicting wild-type protein-ligand binding affinity while the second predicting the mutated protein-ligand binding affinity. The best performing models reported an RMSE value within 0.5 [Formula: see text] 0.6 kcal/mol-1 on an independent test set with an R2 value of 0.87 [Formula: see text] 0.90. We report an improvement in the prediction performance compared to several reported models developed for protein-ligand binding affinity prediction. The obtained models can be used as a complementary method in early-stage drug discovery. They can be applied to rapidly obtain a better overview of the ligand binding affinity changes across protein variants carried by people in the population and narrow down the search space where more time-demanding methods can be used to identify potential leads that achieve a better affinity for all protein variants.
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7
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Aljarf R, Tang S, Pires DEV, Ascher DB. embryoTox: Using Graph-Based Signatures to Predict the Teratogenicity of Small Molecules. J Chem Inf Model 2023; 63:432-441. [PMID: 36595441 DOI: 10.1021/acs.jcim.2c00824] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Teratogenic drugs can lead to extreme fetal malformation and consequently critically influence the fetus's health, yet the teratogenic risks associated with most approved drugs are unknown. Here, we propose a novel predictive tool, embryoTox, which utilizes a graph-based signature representation of the chemical structure of a small molecule to predict and classify molecules likely to be safe during pregnancy. embryoTox was trained and validated using in vitro bioactivity data of over 700 small molecules with characterized teratogenicity effects. Our final model achieved an area under the receiver operating characteristic curve (AUC) of up to 0.96 on 10-fold cross-validation and 0.82 on nonredundant blind tests, outperforming alternative approaches. We believe that our predictive tool will provide a practical resource for optimizing screening libraries to determine effective and safe molecules to use during pregnancy. To provide a simple and integrated platform to rapidly screen for potential safe molecules and their risk factors, we made embryoTox freely available online at https://biosig.lab.uq.edu.au/embryotox/.
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Affiliation(s)
- Raghad Aljarf
- Structural Biology and Bioinformatics, Department of Biochemistry, University of Melbourne, Parkville 3052, Victoria, Australia
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville 3052, Victoria, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne 3004, Victoria, Australia
| | - Simon Tang
- Structural Biology and Bioinformatics, Department of Biochemistry, University of Melbourne, Parkville 3052, Victoria, Australia
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville 3052, Victoria, Australia
| | - Douglas E V Pires
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville 3052, Victoria, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne 3004, Victoria, Australia
- School of Computing and Information Systems, University of Melbourne, Parkville 3052, Victoria, Australia
| | - David B Ascher
- Structural Biology and Bioinformatics, Department of Biochemistry, University of Melbourne, Parkville 3052, Victoria, Australia
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville 3052, Victoria, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne 3004, Victoria, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia 4072, Queensland, Australia
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8
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Ascher DB, Kaminskas LM, Myung Y, Pires DEV. Using Graph-Based Signatures to Guide Rational Antibody Engineering. Methods Mol Biol 2023; 2552:375-397. [PMID: 36346604 DOI: 10.1007/978-1-0716-2609-2_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Antibodies are essential experimental and diagnostic tools and as biotherapeutics have significantly advanced our ability to treat a range of diseases. With recent innovations in computational tools to guide protein engineering, we can now rationally design better antibodies with improved efficacy, stability, and pharmacokinetics. Here, we describe the use of the mCSM web-based in silico suite, which uses graph-based signatures to rapidly identify the structural and functional consequences of mutations, to guide rational antibody engineering to improve stability, affinity, and specificity.
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Affiliation(s)
- David B Ascher
- Structural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- Department of Biochemistry, Cambridge University, Cambridge, UK
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Lisa M Kaminskas
- School of Biological Sciences, University of Queensland, St Lucia, QLD, Australia
| | - Yoochan Myung
- Structural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Douglas E V Pires
- Structural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia.
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.
- School of Computing and Information Systems, University of Melbourne, Parkville, VIC, Australia.
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9
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Zhou Y, Al‐Jarf R, Alavi A, Nguyen TB, Rodrigues CHM, Pires DEV, Ascher DB. kinCSM: Using graph-based signatures to predict small molecule CDK2 inhibitors. Protein Sci 2022; 31:e4453. [PMID: 36305769 PMCID: PMC9597374 DOI: 10.1002/pro.4453] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 11/20/2022]
Abstract
Protein phosphorylation acts as an essential on/off switch in many cellular signaling pathways. This has led to ongoing interest in targeting kinases for therapeutic intervention. Computer‐aided drug discovery has been proven a useful and cost‐effective approach for facilitating prioritization and enrichment of screening libraries, but limited effort has been devoted providing insights on what makes a potent kinase inhibitor. To fill this gap, here we developed kinCSM, an integrative computational tool capable of accurately identifying potent cyclin‐dependent kinase 2 (CDK2) inhibitors, quantitatively predicting CDK2 ligand–kinase inhibition constants (pKi) and classifying different types of inhibitors based on their favorable binding modes. kinCSM predictive models were built using supervised learning and leveraged the concept of graph‐based signatures to capture both physicochemical properties and geometry properties of small molecules. CDK2 inhibitors were accurately identified with Matthew's Correlation Coefficients (MCC) of up to 0.74, and inhibition constants predicted with Pearson's correlation of up to 0.76, both with consistent performances of 0.66 and 0.68 on a nonredundant blind test, respectively. kinCSM was also able to identify the potential type of inhibition for a given molecule, achieving MCC of up to 0.80 on cross‐validation and 0.73 on the blind test. Analyzing the molecular composition of revealed enriched chemical fragments in CDK2 inhibitors and different types of inhibitors, which provides insights into the molecular mechanisms behind ligand–kinase interactions. kinCSM will be an invaluable tool to guide future kinase drug discovery. To aid the fast and accurate screening of CDK2 inhibitors, kinCSM is freely available at https://biosig.lab.uq.edu.au/kin_csm/.
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Affiliation(s)
- Yunzhuo Zhou
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneQueenslandAustralia,Structural Biology and Bioinformatics, Department of BiochemistryUniversity of MelbourneMelbourneVictoriaAustralia,Systems and Computational Biology, Bio21 InstituteUniversity of MelbourneMelbourneVictoriaAustralia,Computational Biology and Clinical InformaticsBaker Heart and Diabetes InstituteMelbourneVictoriaAustralia
| | - Raghad Al‐Jarf
- Structural Biology and Bioinformatics, Department of BiochemistryUniversity of MelbourneMelbourneVictoriaAustralia,Systems and Computational Biology, Bio21 InstituteUniversity of MelbourneMelbourneVictoriaAustralia,Computational Biology and Clinical InformaticsBaker Heart and Diabetes InstituteMelbourneVictoriaAustralia
| | - Azadeh Alavi
- Structural Biology and Bioinformatics, Department of BiochemistryUniversity of MelbourneMelbourneVictoriaAustralia,Systems and Computational Biology, Bio21 InstituteUniversity of MelbourneMelbourneVictoriaAustralia,Computational Biology and Clinical InformaticsBaker Heart and Diabetes InstituteMelbourneVictoriaAustralia
| | - Thanh Binh Nguyen
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneQueenslandAustralia,Structural Biology and Bioinformatics, Department of BiochemistryUniversity of MelbourneMelbourneVictoriaAustralia,Systems and Computational Biology, Bio21 InstituteUniversity of MelbourneMelbourneVictoriaAustralia,Computational Biology and Clinical InformaticsBaker Heart and Diabetes InstituteMelbourneVictoriaAustralia
| | - Carlos H. M. Rodrigues
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneQueenslandAustralia,Structural Biology and Bioinformatics, Department of BiochemistryUniversity of MelbourneMelbourneVictoriaAustralia,Systems and Computational Biology, Bio21 InstituteUniversity of MelbourneMelbourneVictoriaAustralia,Computational Biology and Clinical InformaticsBaker Heart and Diabetes InstituteMelbourneVictoriaAustralia
| | - Douglas E. V. Pires
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneQueenslandAustralia,Structural Biology and Bioinformatics, Department of BiochemistryUniversity of MelbourneMelbourneVictoriaAustralia,Systems and Computational Biology, Bio21 InstituteUniversity of MelbourneMelbourneVictoriaAustralia,Computational Biology and Clinical InformaticsBaker Heart and Diabetes InstituteMelbourneVictoriaAustralia,School of Computing and Information SystemsUniversity of MelbourneMelbourneVictoriaAustralia
| | - David B. Ascher
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneQueenslandAustralia,Structural Biology and Bioinformatics, Department of BiochemistryUniversity of MelbourneMelbourneVictoriaAustralia,Systems and Computational Biology, Bio21 InstituteUniversity of MelbourneMelbourneVictoriaAustralia,Computational Biology and Clinical InformaticsBaker Heart and Diabetes InstituteMelbourneVictoriaAustralia
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10
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Iftkhar S, de Sá AGC, Velloso JPL, Aljarf R, Pires DEV, Ascher DB. cardioToxCSM: A Web Server for Predicting Cardiotoxicity of Small Molecules. J Chem Inf Model 2022; 62:4827-4836. [PMID: 36219164 DOI: 10.1021/acs.jcim.2c00822] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The design of novel, safe, and effective drugs to treat human diseases is a challenging venture, with toxicity being one of the main sources of attrition at later stages of development. Failure due to toxicity incurs a significant increase in costs and time to market, with multiple drugs being withdrawn from the market due to their adverse effects. Cardiotoxicity, for instance, was responsible for the failure of drugs such as fenspiride, propoxyphene, and valdecoxib. While significant effort has been dedicated to mitigate this issue by developing computational approaches that aim to identify molecules likely to be toxic, including quantitative structure-activity relationship models and machine learning methods, current approaches present limited performance and interpretability. To overcome these, we propose a new web-based computational method, cardioToxCSM, which can predict six types of cardiac toxicity outcomes, including arrhythmia, cardiac failure, heart block, hERG toxicity, hypertension, and myocardial infarction, efficiently and accurately. cardioToxCSM was developed using the concept of graph-based signatures, molecular descriptors, toxicophore matchings, and molecular fingerprints, leveraging explainable machine learning, and was validated internally via different cross validation schemes and externally via low-redundancy blind sets. The models presented robust performances with areas under ROC curves of up to 0.898 on 5-fold cross-validation, consistent with metrics on blind tests. Additionally, our models provide interpretation of the predictions by identifying whether substructures that are commonly enriched in toxic compounds were present. We believe cardioToxCSM will provide valuable insight into the potential cardiotoxicity of small molecules early on drug screening efforts. The method is made freely available as a web server at https://biosig.lab.uq.edu.au/cardiotoxcsm.
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Affiliation(s)
- Saba Iftkhar
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia 4072, Queensland, Australia.,Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville 3052, Victoria, Australia.,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne 3004, Victoria, Australia
| | - Alex G C de Sá
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia 4072, Queensland, Australia.,Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville 3052, Victoria, Australia.,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne 3004, Victoria, Australia.,Baker Department of Cardiometabolic Health, Melbourne Medical School, University of Melbourne, Parkville 3010, Victoria, Australia
| | - João P L Velloso
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia 4072, Queensland, Australia.,Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville 3052, Victoria, Australia.,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne 3004, Victoria, Australia
| | - Raghad Aljarf
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville 3052, Victoria, Australia.,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne 3004, Victoria, Australia.,Baker Department of Cardiometabolic Health, Melbourne Medical School, University of Melbourne, Parkville 3010, Victoria, Australia
| | - Douglas E V Pires
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville 3052, Victoria, Australia.,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne 3004, Victoria, Australia.,School of Computing and Information Systems, University of Melbourne, Parkville 3052, Victoria, Australia
| | - David B Ascher
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia 4072, Queensland, Australia.,Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville 3052, Victoria, Australia.,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne 3004, Victoria, Australia.,Baker Department of Cardiometabolic Health, Melbourne Medical School, University of Melbourne, Parkville 3010, Victoria, Australia
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11
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de Sá AGC, Long Y, Portelli S, Pires DEV, Ascher DB. toxCSM: comprehensive prediction of small molecule toxicity profiles. Brief Bioinform 2022; 23:6673851. [PMID: 35998885 DOI: 10.1093/bib/bbac337] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/17/2022] [Accepted: 07/23/2022] [Indexed: 01/29/2023] Open
Abstract
Drug discovery is a lengthy, costly and high-risk endeavour that is further convoluted by high attrition rates in later development stages. Toxicity has been one of the main causes of failure during clinical trials, increasing drug development time and costs. To facilitate early identification and optimisation of toxicity profiles, several computational tools emerged aiming at improving success rates by timely pre-screening drug candidates. Despite these efforts, there is an increasing demand for platforms capable of assessing both environmental as well as human-based toxicity properties at large scale. Here, we present toxCSM, a comprehensive computational platform for the study and optimisation of toxicity profiles of small molecules. toxCSM leverages on the well-established concepts of graph-based signatures, molecular descriptors and similarity scores to develop 36 models for predicting a range of toxicity properties, which can assist in developing safer drugs and agrochemicals. toxCSM achieved an Area Under the Receiver Operating Characteristic (ROC) Curve (AUC) of up to 0.99 and Pearson's correlation coefficients of up to 0.94 on 10-fold cross-validation, with comparable performance on blind test sets, outperforming all alternative methods. toxCSM is freely available as a user-friendly web server and API at http://biosig.lab.uq.edu.au/toxcsm.
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Affiliation(s)
- Alex G C de Sá
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane City, Queensland, 4072, Australia.,Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville, Victoria, 3052, Australia.,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, 3004, Australia.,Baker Department of Cardiometabolic Health, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Yangyang Long
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville, Victoria, 3052, Australia.,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, 3004, Australia.,School of Computing and Information Systems, University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Stephanie Portelli
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane City, Queensland, 4072, Australia.,Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville, Victoria, 3052, Australia.,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, 3004, Australia
| | - Douglas E V Pires
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville, Victoria, 3052, Australia.,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, 3004, Australia.,School of Computing and Information Systems, University of Melbourne, Parkville, Victoria, 3052, Australia
| | - David B Ascher
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane City, Queensland, 4072, Australia.,Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville, Victoria, 3052, Australia.,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, 3004, Australia.,Baker Department of Cardiometabolic Health, University of Melbourne, Parkville, Victoria, 3010, Australia
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12
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Rezende PM, Xavier JS, Ascher DB, Fernandes GR, Pires DEV. Evaluating hierarchical machine learning approaches to classify biological databases. Brief Bioinform 2022; 23:6611916. [PMID: 35724625 PMCID: PMC9310517 DOI: 10.1093/bib/bbac216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 04/29/2022] [Accepted: 05/09/2022] [Indexed: 12/04/2022] Open
Abstract
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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Affiliation(s)
- Pâmela M Rezende
- Universidade Federal de Minas Gerais.,Instituto René Rachou, Fundação Oswaldo Cruz.,Stilingue Inteligência Artificial
| | - Joicymara S Xavier
- Universidade Federal de Minas Gerais.,Instituto René Rachou, Fundação Oswaldo Cruz.,Institute of Agricultural Sciences, Universidade Federal dos Vales do Jequitinhonha e Mucuri
| | - David B Ascher
- School of Chemistry and Molecular Biosciences, University of Queensland.,Systems and Computational Biology, Bio 21 Institute, University of Melbourne.,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute
| | | | - Douglas E V Pires
- Systems and Computational Biology, Bio 21 Institute, University of Melbourne.,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute.,School of Computing and Information Systems, University of Melbourne
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13
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Artificial intelligence in virtual screening: models versus experiments. Drug Discov Today 2022; 27:1913-1923. [PMID: 35597513 DOI: 10.1016/j.drudis.2022.05.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 05/08/2022] [Accepted: 05/12/2022] [Indexed: 12/22/2022]
Abstract
A typical drug discovery project involves identifying active compounds with significant binding potential for selected disease-specific targets. Experimental high-throughput screening (HTS) is a traditional approach to drug discovery, but is expensive and time-consuming when dealing with huge chemical libraries with billions of compounds. The search space can be narrowed down with the use of reliable computational screening approaches. In this review, we focus on various machine-learning (ML) and deep-learning (DL)-based scoring functions developed for solving classification and ranking problems in drug discovery. We highlight studies in which ML and DL models were successfully deployed to identify lead compounds for which the experimental validations are available from bioassay studies.
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14
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Pan Q, Nguyen TB, Ascher DB, Pires DEV. Systematic evaluation of computational tools to predict the effects of mutations on protein stability in the absence of experimental structures. Brief Bioinform 2022; 23:bbac025. [PMID: 35189634 PMCID: PMC9155634 DOI: 10.1093/bib/bbac025] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 01/13/2022] [Accepted: 01/30/2022] [Indexed: 12/26/2022] Open
Abstract
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.
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Affiliation(s)
- Qisheng Pan
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane City, Queensland 4072, Australia
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, 30 Flemington Rd, Parkville, Victoria 3052, Australia
| | - Thanh Binh Nguyen
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane City, Queensland 4072, Australia
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, 30 Flemington Rd, Parkville, Victoria 3052, Australia
| | - David B Ascher
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane City, Queensland 4072, Australia
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, 30 Flemington Rd, Parkville, Victoria 3052, Australia
- Department of Biochemistry, University of Cambridge, 80 Tennis Ct Rd, Cambridge CB2 1GA, UK
| | - Douglas E V Pires
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane City, Queensland 4072, Australia
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, 30 Flemington Rd, Parkville, Victoria 3052, Australia
- School of Computing and Information Systems, University of Melbourne, Melbourne, Victoria 3053, Australia
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15
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Pires DEV, Stubbs KA, Mylne JS, Ascher DB. cropCSM: designing safe and potent herbicides with graph-based signatures. Brief Bioinform 2022; 23:6535680. [PMID: 35211724 PMCID: PMC9155605 DOI: 10.1093/bib/bbac042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 12/11/2022] Open
Abstract
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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Affiliation(s)
- Douglas E V Pires
- School of Computing and Information Systems at the University of Melbourne
| | - Keith A Stubbs
- School of Molecular Sciences at the University of Western Australia
| | - Joshua S Mylne
- Curtin University and Deputy Director of the Centre for Crop and Disease Management
| | - David B Ascher
- University of Queensland, and head of Computational Biology and Clinical Informatics at the Baker Institute and Systems
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16
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Myung Y, Pires DEV, Ascher DB. CSM-AB: graph-based antibody-antigen binding affinity prediction and docking scoring function. Bioinformatics 2022; 38:1141-1143. [PMID: 34734992 DOI: 10.1093/bioinformatics/btab762] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 10/18/2021] [Accepted: 11/01/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Understanding antibody-antigen interactions is key to improving their binding affinities and specificities. While experimental approaches are fundamental for developing new therapeutics, computational methods can provide quick assessment of binding landscapes, guiding experimental design. Despite this, little effort has been devoted to accurately predicting the binding affinity between antibodies and antigens and to develop tailored docking scoring functions for this type of interaction. Here, we developed CSM-AB, a machine learning method capable of predicting antibody-antigen binding affinity by modelling interaction interfaces as graph-based signatures. RESULTS CSM-AB outperformed alternative methods achieving a Pearson's correlation of up to 0.64 on blind tests. We also show CSM-AB can accurately rank near-native poses, working effectively as a docking scoring function. We believe CSM-AB will be an invaluable tool to assist in the development of new immunotherapies. AVAILABILITY AND IMPLEMENTATION CSM-AB is freely available as a user-friendly web interface and API at http://biosig.unimelb.edu.au/csm_ab/datasets. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yoochan Myung
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.,Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Douglas E V Pires
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.,Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, VIC, Australia.,School of Computing and Information Systems, University of Melbourne, Melbourne, VIC, Australia.,School of Chemistry and Molecular Biosciences, University Of Queensland, St Lucia, QLD, Australia
| | - David B Ascher
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.,Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, VIC, Australia.,School of Chemistry and Molecular Biosciences, University Of Queensland, St Lucia, QLD, Australia
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17
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Nguyen TB, Pires DEV, Ascher DB. CSM-carbohydrate: protein-carbohydrate binding affinity prediction and docking scoring function. Brief Bioinform 2021; 23:6457169. [PMID: 34882232 DOI: 10.1093/bib/bbab512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 11/06/2021] [Accepted: 11/08/2021] [Indexed: 12/29/2022] Open
Abstract
Protein-carbohydrate interactions are crucial for many cellular processes but can be challenging to biologically characterise. To improve our understanding and ability to model these molecular interactions, we used a carefully curated set of 370 protein-carbohydrate complexes with experimental structural and biophysical data in order to train and validate a new tool, cutoff scanning matrix (CSM)-carbohydrate, using machine learning algorithms to accurately predict their binding affinity and rank docking poses as a scoring function. Information on both protein and carbohydrate complementarity, in terms of shape and chemistry, was captured using graph-based structural signatures. Across both training and independent test sets, we achieved comparable Pearson's correlations of 0.72 under cross-validation [root mean square error (RMSE) of 1.58 Kcal/mol] and 0.67 on the independent test (RMSE of 1.72 Kcal/mol), providing confidence in the generalisability and robustness of the final model. Similar performance was obtained across mono-, di- and oligosaccharides, further highlighting the applicability of this approach to the study of larger complexes. We show CSM-carbohydrate significantly outperformed previous approaches and have implemented our method and make all data freely available through both a user-friendly web interface and application programming interface, to facilitate programmatic access at http://biosig.unimelb.edu.au/csm_carbohydrate/. We believe CSM-carbohydrate will be an invaluable tool for helping assess docking poses and the effects of mutations on protein-carbohydrate affinity, unravelling important aspects that drive binding recognition.
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Affiliation(s)
- Thanh Binh Nguyen
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.,Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Douglas E V Pires
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.,Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia.,School of Computing and Information Systems, University of Melbourne, Melbourne, Victoria, Australia
| | - David B Ascher
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.,Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.,Department of Biochemistry, University of Cambridge, Cambridge, UK
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18
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Velloso JPL, Ascher DB, Pires DEV. pdCSM-GPCR: predicting potent GPCR ligands with graph-based signatures. BIOINFORMATICS ADVANCES 2021; 1:vbab031. [PMID: 34901870 PMCID: PMC8651072 DOI: 10.1093/bioadv/vbab031] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/30/2021] [Accepted: 11/02/2021] [Indexed: 01/26/2023]
Abstract
MOTIVATION G protein-coupled receptors (GPCRs) can selectively bind to many types of ligands, ranging from light-sensitive compounds, ions, hormones, pheromones and neurotransmitters, modulating cell physiology. Considering their role in many essential cellular processes, they are one of the most targeted protein families, with over a third of all approved drugs modulating GPCR signalling. Despite this, the large diversity of receptors and their multipass transmembrane architectures make the identification and development of novel specific, and safe GPCR ligands a challenge. While computational approaches have the potential to assist GPCR drug development, they have presented limited performance and generalization capabilities. Here, we explored the use of graph-based signatures to develop pdCSM-GPCR, a method capable of rapidly and accurately screening potential GPCR ligands. RESULTS Bioactivity data (IC50, EC50, Ki and Kd) for individual GPCRs were curated. After curation, we used the data for developing predictive models for 36 major GPCR targets, across 4 classes (A, B, C and F). Our models compose the most comprehensive computational resource for GPCR bioactivity prediction to date. Across stratified 10-fold cross-validation and blind tests, our approach achieved Pearson's correlations of up to 0.89, significantly outperforming previous methods. Interpreting our results, we identified common important features of potent GPCRs ligands, which tend to have bicyclic rings, leading to higher levels of aromaticity. We believe pdCSM-GPCR will be an invaluable tool to assist screening efforts, enriching compound libraries and ranking candidates for further experimental validation. AVAILABILITY AND IMPLEMENTATION pdCSM-GPCR predictive models and datasets used have been made available via a freely accessible and easy-to-use web server at http://biosig.unimelb.edu.au/pdcsm_gpcr/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- João Paulo L Velloso
- Fundação Oswaldo Cruz, Instituto René Rachou, Belo Horizonte 30190-009, Brazil,Structural Biology and Bioinformatics, Department of Biochemistry, University of Melbourne, Melbourne 3052, Australia,Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne 3052, Australia,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne 3004, Australia,Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - David B Ascher
- Structural Biology and Bioinformatics, Department of Biochemistry, University of Melbourne, Melbourne 3052, Australia,Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne 3052, Australia,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne 3004, Australia,Baker Department of Cardiometabolic Health, Melbourne Medical School, University of Melbourne, Melbourne 3052, Australia,Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK,To whom correspondence should be addressed. or
| | - Douglas E V Pires
- Structural Biology and Bioinformatics, Department of Biochemistry, University of Melbourne, Melbourne 3052, Australia,Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne 3052, Australia,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne 3004, Australia,School of Computing and Information Systems, University of Melbourne, Melbourne 3053, Australia,To whom correspondence should be addressed. or
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19
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González-Paz L, Hurtado-León ML, Lossada C, Fernández-Materán FV, Vera-Villalobos J, Loroño M, Paz JL, Jeffreys L, Alvarado YJ. Comparative study of the interaction of ivermectin with proteins of interest associated with SARS-CoV-2: A computational and biophysical approach. Biophys Chem 2021; 278:106677. [PMID: 34428682 PMCID: PMC8373590 DOI: 10.1016/j.bpc.2021.106677] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/13/2021] [Accepted: 08/15/2021] [Indexed: 01/18/2023]
Abstract
The SARS-CoV-2 pandemic has accelerated the study of existing drugs. The mixture of homologs called ivermectin (avermectin-B1a [HB1a] + avermectin-B1b [HB1b]) has shown antiviral activity against SARS-CoV-2 in vitro. However, there are few reports on the behavior of each homolog. We investigated the interaction of each homolog with promising targets of interest associated with SARS-CoV-2 infection from a biophysical and computational-chemistry perspective using docking and molecular dynamics. We observed a differential behavior for each homolog, with an affinity of HB1b for viral structures, and of HB1a for host structures considered. The induced disturbances were differential and influenced by the hydrophobicity of each homolog and of the binding pockets. We present the first comparative analysis of the potential theoretical inhibitory effect of both avermectins on biomolecules associated with COVID-19, and suggest that ivermectin through its homologs, has a multiobjective behavior.
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Affiliation(s)
- Lenin González-Paz
- Universidad del Zulia (LUZ), Facultad Experimental de Ciencias (FEC), Departamento de Biología, Laboratorio de Genética y Biología Molecular (LGBM), 4001 Maracaibo, Venezuela; Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Estudios Botánicos y Agroforestales (CEBA), Laboratorio de Protección Vegetal (LPV), 4001 Maracaibo, Venezuela.
| | - María Laura Hurtado-León
- Universidad del Zulia (LUZ), Facultad Experimental de Ciencias (FEC), Departamento de Biología, Laboratorio de Genética y Biología Molecular (LGBM), 4001 Maracaibo, Venezuela
| | - Carla Lossada
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Investigación y Tecnología de Materiales (CITeMA), Laboratorio de Caracterización Molecular y Biomolecular, 4001 Maracaibo, Venezuela
| | - Francelys V Fernández-Materán
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Investigación y Tecnología de Materiales (CITeMA), Laboratorio de Caracterización Molecular y Biomolecular, 4001 Maracaibo, Venezuela
| | - Joan Vera-Villalobos
- Facultad de Ciencias Naturales y Matemáticas, Departamento de Química y Ciencias Ambientales, Laboratorio de Análisis Químico Instrumental (LAQUINS), Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
| | - Marcos Loroño
- Departamento Académico de Química Analítica e Instrumental, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - J L Paz
- Departamento Académico de Química Inorgánica, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Laura Jeffreys
- Centre for Drugs and Diagnostics, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Ysaias J Alvarado
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Investigación y Tecnología de Materiales (CITeMA), Laboratorio de Caracterización Molecular y Biomolecular, 4001 Maracaibo, Venezuela.
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20
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da Silva BM, Myung Y, Ascher DB, Pires DEV. epitope3D: a machine learning method for conformational B-cell epitope prediction. Brief Bioinform 2021; 23:6407730. [PMID: 34676398 DOI: 10.1093/bib/bbab423] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/25/2021] [Accepted: 09/14/2021] [Indexed: 11/13/2022] Open
Abstract
The ability to identify antigenic determinants of pathogens, or epitopes, is fundamental to guide rational vaccine development and immunotherapies, which are particularly relevant for rapid pandemic response. A range of computational tools has been developed over the past two decades to assist in epitope prediction; however, they have presented limited performance and generalization, particularly for the identification of conformational B-cell epitopes. Here, we present epitope3D, a novel scalable machine learning method capable of accurately identifying conformational epitopes trained and evaluated on the largest curated epitope data set to date. Our method uses the concept of graph-based signatures to model epitope and non-epitope regions as graphs and extract distance patterns that are used as evidence to train and test predictive models. We show epitope3D outperforms available alternative approaches, achieving Mathew's Correlation Coefficient and F1-scores of 0.55 and 0.57 on cross-validation and 0.45 and 0.36 during independent blind tests, respectively.
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Affiliation(s)
- Bruna Moreira da Silva
- Structural Biology and Bioinformatics, Department of Biochemistry, University of Melbourne, Melbourne, Victoria, Australia.,Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia.,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.,School of Computing and Information Systems, University of Melbourne, Melbourne, Victoria, Australia
| | - YooChan Myung
- Structural Biology and Bioinformatics, Department of Biochemistry, University of Melbourne, Melbourne, Victoria, Australia.,Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia.,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.,Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, Victoria, Australia
| | - David B Ascher
- Structural Biology and Bioinformatics, Department of Biochemistry, University of Melbourne, Melbourne, Victoria, Australia.,Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia.,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.,Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, Victoria, Australia.,Department of Biochemistry, University of Cambridge, 80 Tennis Ct Rd, Cambridge CB2 1GA, UK
| | - Douglas E V Pires
- Structural Biology and Bioinformatics, Department of Biochemistry, University of Melbourne, Melbourne, Victoria, Australia.,Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia.,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.,School of Computing and Information Systems, University of Melbourne, Melbourne, Victoria, Australia
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21
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Zhou Y, Portelli S, Pat M, Rodrigues CH, Nguyen TB, Pires DE, Ascher DB. Structure-guided machine learning prediction of drug resistance mutations in Abelson 1 kinase. Comput Struct Biotechnol J 2021; 19:5381-5391. [PMID: 34667533 PMCID: PMC8495037 DOI: 10.1016/j.csbj.2021.09.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/15/2021] [Accepted: 09/15/2021] [Indexed: 02/02/2023] Open
Abstract
Kinases play crucial roles in cellular signalling and biological processes with their dysregulation associated with diseases, including cancers. Kinase inhibitors, most notably those targeting ABeLson 1 (ABL1) kinase in chronic myeloid leukemia, have had a significant impact on cancer survival, yet emergence of resistance mutations can reduce their effectiveness, leading to therapeutic failure. Limited effort, however, has been devoted to developing tools to accurately identify ABL1 resistance mutations, as well as providing insights into their molecular mechanisms. Here we investigated the structural basis of ABL1 mutations modulating binding affinity of eight FDA-approved drugs. We found mutations impair affinity of type I and type II inhibitors differently and used this insight to developed a novel web-based diagnostic tool, SUSPECT-ABL, to pre-emptively predict resistance profiles and binding free-energy changes (ΔΔG) of all possible ABL1 mutations against inhibitors with different binding modes. Resistance mutations in ABL1 were successfully identified, achieving a Matthew's Correlation Coefficient of up to 0.73 and the resulting change in ligand binding affinity with a Pearson's correlation of up to 0.77, with performances consistent across non-redundant blind tests. Through an in silico saturation mutagenesis, our tool has identified possibly emerging resistance mutations, which offers opportunities for in vivo experimental validation. We believe SUSPECT-ABL will be an important tool not just for improving precision medicine efforts, but for facilitating the development of next-generation inhibitors that are less prone to resistance. We have made our tool freely available at http://biosig.unimelb.edu.au/suspect_abl/.
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Affiliation(s)
- Yunzhuo Zhou
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Stephanie Portelli
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Megan Pat
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Carlos H.M. Rodrigues
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Thanh-Binh Nguyen
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
- Baker Department of Cardiometabolic Health, Melbourne Medical School, University of Melbourne, Melbourne, Victoria, Australia
| | - Douglas E.V. Pires
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
- School of Computing and Information Systems, University of Melbourne, Melbourne, Victoria, Australia
| | - David B. Ascher
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
- Baker Department of Cardiometabolic Health, Melbourne Medical School, University of Melbourne, Melbourne, Victoria, Australia
- Department of Biochemistry, University of Cambridge, 80 Tennis Ct Rd, Cambridge CB2 1GA, UK
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22
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Gupta R, Srivastava D, Sahu M, Tiwari S, Ambasta RK, Kumar P. Artificial intelligence to deep learning: machine intelligence approach for drug discovery. Mol Divers 2021; 25:1315-1360. [PMID: 33844136 PMCID: PMC8040371 DOI: 10.1007/s11030-021-10217-3] [Citation(s) in RCA: 253] [Impact Index Per Article: 84.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/22/2021] [Indexed: 02/06/2023]
Abstract
Drug designing and development is an important area of research for pharmaceutical companies and chemical scientists. However, low efficacy, off-target delivery, time consumption, and high cost impose a hurdle and challenges that impact drug design and discovery. Further, complex and big data from genomics, proteomics, microarray data, and clinical trials also impose an obstacle in the drug discovery pipeline. Artificial intelligence and machine learning technology play a crucial role in drug discovery and development. In other words, artificial neural networks and deep learning algorithms have modernized the area. Machine learning and deep learning algorithms have been implemented in several drug discovery processes such as peptide synthesis, structure-based virtual screening, ligand-based virtual screening, toxicity prediction, drug monitoring and release, pharmacophore modeling, quantitative structure-activity relationship, drug repositioning, polypharmacology, and physiochemical activity. Evidence from the past strengthens the implementation of artificial intelligence and deep learning in this field. Moreover, novel data mining, curation, and management techniques provided critical support to recently developed modeling algorithms. In summary, artificial intelligence and deep learning advancements provide an excellent opportunity for rational drug design and discovery process, which will eventually impact mankind. The primary concern associated with drug design and development is time consumption and production cost. Further, inefficiency, inaccurate target delivery, and inappropriate dosage are other hurdles that inhibit the process of drug delivery and development. With advancements in technology, computer-aided drug design integrating artificial intelligence algorithms can eliminate the challenges and hurdles of traditional drug design and development. Artificial intelligence is referred to as superset comprising machine learning, whereas machine learning comprises supervised learning, unsupervised learning, and reinforcement learning. Further, deep learning, a subset of machine learning, has been extensively implemented in drug design and development. The artificial neural network, deep neural network, support vector machines, classification and regression, generative adversarial networks, symbolic learning, and meta-learning are examples of the algorithms applied to the drug design and discovery process. Artificial intelligence has been applied to different areas of drug design and development process, such as from peptide synthesis to molecule design, virtual screening to molecular docking, quantitative structure-activity relationship to drug repositioning, protein misfolding to protein-protein interactions, and molecular pathway identification to polypharmacology. Artificial intelligence principles have been applied to the classification of active and inactive, monitoring drug release, pre-clinical and clinical development, primary and secondary drug screening, biomarker development, pharmaceutical manufacturing, bioactivity identification and physiochemical properties, prediction of toxicity, and identification of mode of action.
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Affiliation(s)
- Rohan Gupta
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Devesh Srivastava
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Mehar Sahu
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Swati Tiwari
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Rashmi K Ambasta
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Shahbad Daulatpur, Bawana Road, Delhi, 110042, India.
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23
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Rodrigues CHM, Pires DEV, Ascher DB. mmCSM-PPI: predicting the effects of multiple point mutations on protein-protein interactions. Nucleic Acids Res 2021; 49:W417-W424. [PMID: 33893812 PMCID: PMC8262703 DOI: 10.1093/nar/gkab273] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/18/2021] [Accepted: 04/15/2021] [Indexed: 11/16/2022] Open
Abstract
Protein-protein interactions play a crucial role in all cellular functions and biological processes and mutations leading to their disruption are enriched in many diseases. While a number of computational methods to assess the effects of variants on protein-protein binding affinity have been proposed, they are in general limited to the analysis of single point mutations and have been shown to perform poorly on independent test sets. Here, we present mmCSM-PPI, a scalable and effective machine learning model for accurately assessing changes in protein-protein binding affinity caused by single and multiple missense mutations. We expanded our well-established graph-based signatures in order to capture physicochemical and geometrical properties of multiple wild-type residue environments and integrated them with substitution scores and dynamics terms from normal mode analysis. mmCSM-PPI was able to achieve a Pearson's correlation of up to 0.75 (RMSE = 1.64 kcal/mol) under 10-fold cross-validation and 0.70 (RMSE = 2.06 kcal/mol) on a non-redundant blind test, outperforming existing methods. Our method is freely available as a user-friendly and easy-to-use web server and API at http://biosig.unimelb.edu.au/mmcsm_ppi.
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Affiliation(s)
- Carlos H M Rodrigues
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Structural Biology and Bioinformatics, Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, Victoria, Australia
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Douglas E V Pires
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Structural Biology and Bioinformatics, Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, Victoria, Australia
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
- School of Computing and Information Systems, University of Melbourne, Melbourne, Victoria, Australia
| | - David B Ascher
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Structural Biology and Bioinformatics, Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, Victoria, Australia
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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24
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Al-Jarf R, de Sá AGC, Pires DEV, Ascher DB. pdCSM-cancer: Using Graph-Based Signatures to Identify Small Molecules with Anticancer Properties. J Chem Inf Model 2021; 61:3314-3322. [PMID: 34213323 PMCID: PMC8317153 DOI: 10.1021/acs.jcim.1c00168] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
The development of
new, effective, and safe drugs to treat cancer
remains a challenging and time-consuming task due to limited hit rates,
restraining subsequent development efforts. Despite the impressive
progress of quantitative structure–activity relationship and
machine learning-based models that have been developed to predict
molecule pharmacodynamics and bioactivity, they have had mixed success
at identifying compounds with anticancer properties against multiple
cell lines. Here, we have developed a novel predictive tool, pdCSM-cancer,
which uses a graph-based signature representation of the chemical
structure of a small molecule in order to accurately predict molecules
likely to be active against one or multiple cancer cell lines. pdCSM-cancer
represents the most comprehensive anticancer bioactivity prediction
platform developed till date, comprising trained and validated models
on experimental data of the growth inhibition concentration (GI50%)
effects, including over 18,000 compounds, on 9 tumor types and 74
distinct cancer cell lines. Across 10-fold cross-validation, it achieved
Pearson’s correlation coefficients of up to 0.74 and comparable
performance of up to 0.67 across independent, non-redundant blind
tests. Leveraging the insights from these cell line-specific models,
we developed a generic predictive model to identify molecules active
in at least 60 cell lines. Our final model achieved an area under
the receiver operating characteristic curve (AUC) of up to 0.94 on
10-fold cross-validation and up to 0.94 on independent non-redundant
blind tests, outperforming alternative approaches. We believe that
our predictive tool will provide a valuable resource to optimizing
and enriching screening libraries for the identification of effective
and safe anticancer molecules. To provide a simple and integrated
platform to rapidly screen for potential biologically active molecules
with favorable anticancer properties, we made pdCSM-cancer freely
available online at http://biosig.unimelb.edu.au/pdcsm_cancer.
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Affiliation(s)
- Raghad Al-Jarf
- Structural Biology and Bioinformatics, Department of Biochemistry, University of Melbourne, Parkville 3052, Victoria, Australia.,Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville 3052, Victoria, Australia.,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne 3004, Victoria, Australia
| | - Alex G C de Sá
- Structural Biology and Bioinformatics, Department of Biochemistry, University of Melbourne, Parkville 3052, Victoria, Australia.,Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville 3052, Victoria, Australia.,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne 3004, Victoria, Australia.,Baker Department of Cardiometabolic Health, Melbourne Medical School, University of Melbourne, Parkville 3010, Victoria, Australia
| | - Douglas E V Pires
- Structural Biology and Bioinformatics, Department of Biochemistry, University of Melbourne, Parkville 3052, Victoria, Australia.,Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville 3052, Victoria, Australia.,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne 3004, Victoria, Australia.,School of Computing and Information Systems, University of Melbourne, Parkville 3052, Victoria, Australia
| | - David B Ascher
- Structural Biology and Bioinformatics, Department of Biochemistry, University of Melbourne, Parkville 3052, Victoria, Australia.,Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville 3052, Victoria, Australia.,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne 3004, Victoria, Australia.,Baker Department of Cardiometabolic Health, Melbourne Medical School, University of Melbourne, Parkville 3010, Victoria, Australia.,Department of Biochemistry, University of Cambridge, 80 Tennis Ct Rd, Cambridge CB2 1GA, United Kingdom
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25
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Qin T, Zhu Z, Wang XS, Xia J, Wu S. Computational representations of protein-ligand interfaces for structure-based virtual screening. Expert Opin Drug Discov 2021; 16:1175-1192. [PMID: 34011222 DOI: 10.1080/17460441.2021.1929921] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Introduction: Structure-based virtual screening (SBVS) is an essential strategy for hit identification. SBVS primarily uses molecular docking, which exploits the protein-ligand binding mode and associated affinity score for compound ranking. Previous studies have shown that computational representation of protein-ligand interfaces and the later establishment of machine learning models are efficacious in improving the accuracy of SBVS.Areas covered: The authors review the computational methods for representing protein-ligand interfaces, which include the traditional ones that use deliberately designed fingerprints and descriptors and the more recent methods that automatically extract features with deep learning. The effects of these methods on the performance of machine learning models are briefly discussed. Additionally, case studies that applied various computational representations to machine learning are cited with remarks.Expert opinion: It has become a trend to extract binding features automatically by deep learning, which uses a completely end-to-end representation. However, there is still plenty of scope for improvement . The interpretability of deep-learning models, the organization of data management, the quantity and quality of available data, and the optimization of hyperparameters could impact the accuracy of feature extraction. In addition, other important structural factors such as water molecules and protein flexibility should be considered.
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Affiliation(s)
- Tong Qin
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zihao Zhu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiang Simon Wang
- Artificial Intelligence and Drug Discovery Core Laboratory for District of Columbia Center for AIDS Research (DC CFAR), Department of Pharmaceutical Sciences, College of Pharmacy, Howard University, U.S.A
| | - Jie Xia
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Song Wu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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26
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Bisphenol A Inhibits the Transporter Function of the Blood-Brain Barrier by Directly Interacting with the ABC Transporter Breast Cancer Resistance Protein (BCRP). Int J Mol Sci 2021; 22:ijms22115534. [PMID: 34073890 PMCID: PMC8197233 DOI: 10.3390/ijms22115534] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/16/2021] [Accepted: 05/19/2021] [Indexed: 02/07/2023] Open
Abstract
The breast cancer resistance protein (BCRP) is an important efflux transporter in the blood-brain barrier (BBB), protecting the brain from a wide range of substances. In this study, we investigated if BCRP function is affected by bisphenol A (BPA), a high production volume chemical used in common consumer products, as well as by bisphenol F (BPF) and bisphenol S (BPS), which are used to substitute BPA. We employed a transwell-based in vitro cell model of iPSC-derived brain microvascular endothelial cells, where BCRP function was assessed by measuring the intracellular accumulation of its substrate Hoechst 33342. Additionally, we used in silico modelling to predict if the bisphenols could directly interact with BCRP. Our results showed that BPA significantly inhibits the transport function of BCRP. Additionally, BPA was predicted to bind to the cavity that is targeted by known BCRP inhibitors. Taken together, our findings demonstrate that BPA inhibits BCRP function in vitro, probably by direct interaction with the transporter. This effect might contribute to BPA’s known impact on neurodevelopment.
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27
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Rayka M, Karimi-Jafari MH, Firouzi R. ET-score: Improving Protein-ligand Binding Affinity Prediction Based on Distance-weighted Interatomic Contact Features Using Extremely Randomized Trees Algorithm. Mol Inform 2021; 40:e2060084. [PMID: 34021703 DOI: 10.1002/minf.202060084] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 04/20/2021] [Indexed: 12/15/2022]
Abstract
The molecular docking simulation is a key computational tool in modern drug discovery research that its predictive performance strongly depends on the employed scoring functions. Many recent studies have shown that the application of machine learning algorithms in the development of scoring functions has led to a significant improvement in docking performance. In this work, we introduce a new machine learning (ML) based scoring function called ET-Score, which employs the distance-weighted interatomic contacts between atom type pairs of the ligand and the protein for featurizing protein-ligand complexes and Extremely Randomized Trees algorithm for the training process. The performance of ET-Score is compared with some successful ML-based scoring functions and several popular classical scoring functions on the PDBbind 2016v core set. It is shown that our ET-Score model (with Pearson's correlation of 0.827 and RMSE of 1.332) achieves very good performance in comparison with most of the ML-based scoring functions and all classical scoring functions despite its extremely low computational cost. ET-Score's codes are freely available on the web at https://github.com/miladrayka/ET_Score.
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Affiliation(s)
- Milad Rayka
- Department of Physical Chemistry, Chemistry and Chemical Engineering Research Center of Iran, Tehran, Iran
| | | | - Rohoullah Firouzi
- Department of Physical Chemistry, Chemistry and Chemical Engineering Research Center of Iran, Tehran, Iran
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28
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Wiryaman T, Toor N. Cryo-EM structure of a thermostable bacterial nanocompartment. IUCRJ 2021; 8:342-350. [PMID: 33953921 PMCID: PMC8086157 DOI: 10.1107/s2052252521001949] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 02/18/2021] [Indexed: 05/21/2023]
Abstract
Protein nanocompartments are widespread in bacteria and archaea, but their functions are not yet well understood. Here, the cryo-EM structure of a nanocompartment from the thermophilic bacterium Thermotoga maritima is reported at 2.0 Å resolution. The high resolution of this structure shows that interactions in the E-loop domain may be important for the thermostability of the nanocompartment assembly. Also, the channels at the fivefold axis, threefold axis and dimer interface are assessed for their ability to transport iron. Finally, an unexpected flavin ligand was identified on the exterior of the shell, indicating that this nanocompartment may also play a direct role in iron metabolism.
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Affiliation(s)
- Timothy Wiryaman
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Navtej Toor
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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29
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Synthesis, characterization, molecular modeling and preliminary biochemical evaluation of new copper (II) mixed-ligand complexes. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129695] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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30
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Pires DEV, Veloso WNP, Myung Y, Rodrigues CHM, Silk M, Rezende PM, Silva F, Xavier JS, Velloso JPL, da Silveira CH, Ascher DB. EasyVS: a user-friendly web-based tool for molecule library selection and structure-based virtual screening. Bioinformatics 2021; 36:4200-4202. [PMID: 32399551 DOI: 10.1093/bioinformatics/btaa480] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 04/01/2020] [Accepted: 05/05/2020] [Indexed: 11/14/2022] Open
Abstract
SUMMARY EasyVS is a web-based platform built to simplify molecule library selection and virtual screening. With an intuitive interface, the tool allows users to go from selecting a protein target with a known structure and tailoring a purchasable molecule library to performing and visualizing docking in a few clicks. Our system also allows users to filter screening libraries based on molecule properties, cluster molecules by similarity and personalize docking parameters. AVAILABILITY AND IMPLEMENTATION EasyVS is freely available as an easy-to-use web interface at http://biosig.unimelb.edu.au/easyvs. CONTACT douglas.pires@unimelb.edu.au or david.ascher@unimelb.edu.au. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Douglas E V Pires
- School of Computing and Information Systems, University of Melbourne, Melbourne 3010, Australia.,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne 3004, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne 3010, Australia
| | - Wandré N P Veloso
- Institute of Technological Sciences, Universidade Federal de Itajubá, Itabira 35903-087, Brazil
| | - YooChan Myung
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne 3004, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne 3010, Australia
| | - Carlos H M Rodrigues
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne 3004, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne 3010, Australia
| | - Michael Silk
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne 3004, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne 3010, Australia
| | - Pâmela M Rezende
- Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-002, Brazil
| | - Francislon Silva
- Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-002, Brazil
| | - Joicymara S Xavier
- Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-002, Brazil.,Instituto de Ciências Agrárias, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Unaí 38610-000, Brazil
| | - João P L Velloso
- Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-002, Brazil
| | - Carlos H da Silveira
- Institute of Technological Sciences, Universidade Federal de Itajubá, Itabira 35903-087, Brazil
| | - David B Ascher
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne 3004, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne 3010, Australia.,Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
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31
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Fang XZ, Fang SQ, Ye ZQ, Liu D, Zhao KL, Jin CW. NRT1.1 Dual-Affinity Nitrate Transport/Signalling and its Roles in Plant Abiotic Stress Resistance. FRONTIERS IN PLANT SCIENCE 2021; 12:715694. [PMID: 34497626 PMCID: PMC8420879 DOI: 10.3389/fpls.2021.715694] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/02/2021] [Indexed: 05/04/2023]
Abstract
NRT1.1 is the first nitrate transport protein cloned in plants and has both high- and low-affinity functions. It imports and senses nitrate, which is modulated by the phosphorylation on Thr101 (T101). Structural studies have revealed that the phosphorylation of T101 either induces dimer decoupling or increases structural flexibility within the membrane, thereby switching the NRT1.1 protein from a low- to high-affinity state. Further studies on the adaptive regulation of NRT1.1 in fluctuating nitrate conditions have shown that, at low nitrate concentrations, nitrate binding only at the high-affinity monomer initiates NRT1.1 dimer decoupling and priming of the T101 site for phosphorylation activated by CIPK23, which functions as a high-affinity nitrate transceptor. However, nitrate binding in both monomers retains the unmodified NRT1.1, maintaining the low-affinity mode. This NRT1.1-mediated nitrate signalling and transport may provide a key to improving the efficiency of plant nitrogen use. However, recent studies have revealed that NRT1.1 is extensively involved in plant tolerance of several adverse environmental conditions. In this context, we summarise the recent progress in the molecular mechanisms of NRT1.1 dual-affinity nitrate transport/signalling and focus on its expected and unexpected roles in plant abiotic stress resistance and their regulation processes.
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Affiliation(s)
- Xian Zhi Fang
- Key Laboratory of Soil Contamination Bioremediation of Zhejiang Province, State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Zhejiang, China
- *Correspondence: Xian Zhi Fang,
| | - Shu Qin Fang
- Key Laboratory of Soil Contamination Bioremediation of Zhejiang Province, State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Zhejiang, China
| | - Zheng Qian Ye
- Key Laboratory of Soil Contamination Bioremediation of Zhejiang Province, State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Zhejiang, China
| | - Dan Liu
- Key Laboratory of Soil Contamination Bioremediation of Zhejiang Province, State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Zhejiang, China
| | - Ke Li Zhao
- Key Laboratory of Soil Contamination Bioremediation of Zhejiang Province, State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Zhejiang, China
| | - Chong Wei Jin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Natural Resources and Environmental Science, Zhejiang University, Hangzhou, China
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32
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Decherchi S, Cavalli A. Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation. Chem Rev 2020; 120:12788-12833. [PMID: 33006893 PMCID: PMC8011912 DOI: 10.1021/acs.chemrev.0c00534] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Indexed: 12/19/2022]
Abstract
Computational studies play an increasingly important role in chemistry and biophysics, mainly thanks to improvements in hardware and algorithms. In drug discovery and development, computational studies can reduce the costs and risks of bringing a new medicine to market. Computational simulations are mainly used to optimize promising new compounds by estimating their binding affinity to proteins. This is challenging due to the complexity of the simulated system. To assess the present and future value of simulation for drug discovery, we review key applications of advanced methods for sampling complex free-energy landscapes at near nonergodicity conditions and for estimating the rate coefficients of very slow processes of pharmacological interest. We outline the statistical mechanics and computational background behind this research, including methods such as steered molecular dynamics and metadynamics. We review recent applications to pharmacology and drug discovery and discuss possible guidelines for the practitioner. Recent trends in machine learning are also briefly discussed. Thanks to the rapid development of methods for characterizing and quantifying rare events, simulation's role in drug discovery is likely to expand, making it a valuable complement to experimental and clinical approaches.
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Affiliation(s)
- Sergio Decherchi
- Computational
and Chemical Biology, Fondazione Istituto
Italiano di Tecnologia, 16163 Genoa, Italy
| | - Andrea Cavalli
- Computational
and Chemical Biology, Fondazione Istituto
Italiano di Tecnologia, 16163 Genoa, Italy
- Department
of Pharmacy and Biotechnology, University
of Bologna, 40126 Bologna, Italy
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33
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Souza Silva JA, Tunes LG, Coimbra RS, Ascher DB, Pires DEV, Monte-Neto RL. Unveiling six potent and highly selective antileishmanial agents via the open source compound collection 'Pathogen Box' against antimony-sensitive and -resistant Leishmania braziliensis. Biomed Pharmacother 2020; 133:111049. [PMID: 33378956 DOI: 10.1016/j.biopha.2020.111049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/15/2020] [Accepted: 11/19/2020] [Indexed: 02/06/2023] Open
Abstract
Despite all efforts to provide new chemical entities to tackle leishmaniases, we are still dependent on a the limited drug arsenal, together with drawbacks like toxicity and drug-resistant parasites. Collaborative drug discovery emerged as an option to speed up the way to find alternative antileishmanial agents. This is the case of Medicines for Malaria Ventures - MMV, that promotes an open source drug discovery initiative to fight diseases worldwide. Here, we screened 400 compounds from 'Pathogen Box' (PBox) collection against Leishmania braziliensis, the main etiological agent of cutaneous leishmaniasis in Brazil. Twenty-three compounds were able to inhibit ≥ 80 % L. braziliensis growth at 5 μM. Six out of the PBox selected 23 compounds were found to be highly selective against L. braziliensis intracellular amastigotes with selectivity index varying from > 104 to > 746 and IC50s ranging from 47 to 480 nM. The compounds were also active against antimony-resistant L. braziliensis isolated from the field or laboratory selected mutants, revealing the potential on treating patients infected with drug resistant parasites. Most of the selected compounds were known to be active against kinetoplastids, however, two compounds (MMV688703 and MMV676477) were part of toxoplasmosis and tuberculosis 'PBox' disease set, reinforcing the potential of phenotyping screening to unveil drug repurposing. Here we applied a computational prediction of pharmacokinetic properties using the ADMET predictor pkCSM (http://biosig.unimelb.edu.au/pkcsm/). The tool offered clues on potential drug development needs and can support further in vivo studies. Molecular docking analysis identified CRK3 (LbrM.35.0660), CYP450 (LbrM.30.3580) and PKA (LbrM.18.1180) as L. braziliensis targets for MMV676604, MMV688372 and MMV688703, respectively. Compounds from 'Pathogen Box' thus represents a new hope for novel (or repurposed) small molecules source to tackle leishmaniases.
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Affiliation(s)
- Juliano A Souza Silva
- Instituto René Rachou - Fiocruz Minas, Av. Augusto de Lima, 1715, Belo Horizonte, 30190-009, MG, Brazil.
| | - Luiza G Tunes
- Instituto René Rachou - Fiocruz Minas, Av. Augusto de Lima, 1715, Belo Horizonte, 30190-009, MG, Brazil.
| | - Roney S Coimbra
- Instituto René Rachou - Fiocruz Minas, Av. Augusto de Lima, 1715, Belo Horizonte, 30190-009, MG, Brazil.
| | - David B Ascher
- Structural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, The University of Melbourne, Bio21 Institute, 30 Flemington Rd, Parkville, VIC 3052, Melbourne, Australia; Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, VIC 3004, Melbourne, Australia.
| | - Douglas E V Pires
- Instituto René Rachou - Fiocruz Minas, Av. Augusto de Lima, 1715, Belo Horizonte, 30190-009, MG, Brazil; School of Computing and Information Systems, The University of Melbourne, Doug McDonell Building, VIC 3010, Parkville, Melbourne, Australia.
| | - Rubens L Monte-Neto
- Instituto René Rachou - Fiocruz Minas, Av. Augusto de Lima, 1715, Belo Horizonte, 30190-009, MG, Brazil.
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Bao J, He X, Zhang JZ. Development of a New Scoring Function for Virtual Screening: APBScore. J Chem Inf Model 2020; 60:6355-6365. [DOI: 10.1021/acs.jcim.0c00474] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Jingxiao Bao
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry, NYU Shanghai, Shanghai 200062, China
| | - John Z.H. Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry, NYU Shanghai, Shanghai 200062, China
- Department of Chemistry, New York University, New York, New York 10003, United States
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
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Pires DEV, Rodrigues CHM, Ascher DB. mCSM-membrane: predicting the effects of mutations on transmembrane proteins. Nucleic Acids Res 2020; 48:W147-W153. [PMID: 32469063 PMCID: PMC7319563 DOI: 10.1093/nar/gkaa416] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/04/2020] [Accepted: 05/28/2020] [Indexed: 12/17/2022] Open
Abstract
Significant efforts have been invested into understanding and predicting the molecular consequences of mutations in protein coding regions, however nearly all approaches have been developed using globular, soluble proteins. These methods have been shown to poorly translate to studying the effects of mutations in membrane proteins. To fill this gap, here we report, mCSM-membrane, a user-friendly web server that can be used to analyse the impacts of mutations on membrane protein stability and the likelihood of them being disease associated. mCSM-membrane derives from our well-established mutation modelling approach that uses graph-based signatures to model protein geometry and physicochemical properties for supervised learning. Our stability predictor achieved correlations of up to 0.72 and 0.67 (on cross validation and blind tests, respectively), while our pathogenicity predictor achieved a Matthew's Correlation Coefficient (MCC) of up to 0.77 and 0.73, outperforming previously described methods in both predicting changes in stability and in identifying pathogenic variants. mCSM-membrane will be an invaluable and dedicated resource for investigating the effects of single-point mutations on membrane proteins through a freely available, user friendly web server at http://biosig.unimelb.edu.au/mcsm_membrane.
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Affiliation(s)
- Douglas E V Pires
- Computational Biology and Clinical Informatics, Baker Institute, Melbourne, Victoria 3004, Australia.,Structural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, VIC, 3052, Australia.,School of Computing and Information Systems, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Carlos H M Rodrigues
- Computational Biology and Clinical Informatics, Baker Institute, Melbourne, Victoria 3004, Australia.,Structural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, VIC, 3052, Australia
| | - David B Ascher
- Computational Biology and Clinical Informatics, Baker Institute, Melbourne, Victoria 3004, Australia.,Structural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, VIC, 3052, Australia.,Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
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Myung Y, Rodrigues CHM, Ascher DB, Pires DEV. mCSM-AB2: guiding rational antibody design using graph-based signatures. Bioinformatics 2020; 36:1453-1459. [PMID: 31665262 DOI: 10.1093/bioinformatics/btz779] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 10/07/2019] [Accepted: 10/23/2019] [Indexed: 12/11/2022] Open
Abstract
MOTIVATION A lack of accurate computational tools to guide rational mutagenesis has made affinity maturation a recurrent challenge in antibody (Ab) development. We previously showed that graph-based signatures can be used to predict the effects of mutations on Ab binding affinity. RESULTS Here we present an updated and refined version of this approach, mCSM-AB2, capable of accurately modelling the effects of mutations on Ab-antigen binding affinity, through the inclusion of evolutionary and energetic terms. Using a new and expanded database of over 1800 mutations with experimental binding measurements and structural information, mCSM-AB2 achieved a Pearson's correlation of 0.73 and 0.77 across training and blind tests, respectively, outperforming available methods currently used for rational Ab engineering. AVAILABILITY AND IMPLEMENTATION mCSM-AB2 is available as a user-friendly and freely accessible web server providing rapid analysis of both individual mutations or the entire binding interface to guide rational antibody affinity maturation at http://biosig.unimelb.edu.au/mcsm_ab2. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yoochan Myung
- Department of Biochemistry and Molecular Biology.,ACRF Facility for Innovative Cancer Drug Discovery, Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia.,Structural Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia
| | - Carlos H M Rodrigues
- Department of Biochemistry and Molecular Biology.,ACRF Facility for Innovative Cancer Drug Discovery, Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia.,Structural Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia
| | - David B Ascher
- Department of Biochemistry and Molecular Biology.,ACRF Facility for Innovative Cancer Drug Discovery, Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia.,Structural Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia.,Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Douglas E V Pires
- Department of Biochemistry and Molecular Biology.,ACRF Facility for Innovative Cancer Drug Discovery, Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia.,Structural Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia.,School of Computing and Information Systems, University of Melbourne, Melbourne, VIC 3010, Australia
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Rodrigues CHM, Pires DEV, Ascher DB. DynaMut2: Assessing changes in stability and flexibility upon single and multiple point missense mutations. Protein Sci 2020; 30:60-69. [PMID: 32881105 PMCID: PMC7737773 DOI: 10.1002/pro.3942] [Citation(s) in RCA: 207] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 12/11/2022]
Abstract
Predicting the effect of missense variations on protein stability and dynamics is important for understanding their role in diseases, and the link between protein structure and function. Approaches to estimate these changes have been proposed, but most only consider single‐point missense variants and a static state of the protein, with those that incorporate dynamics are computationally expensive. Here we present DynaMut2, a web server that combines Normal Mode Analysis (NMA) methods to capture protein motion and our graph‐based signatures to represent the wildtype environment to investigate the effects of single and multiple point mutations on protein stability and dynamics. DynaMut2 was able to accurately predict the effects of missense mutations on protein stability, achieving Pearson's correlation of up to 0.72 (RMSE: 1.02 kcal/mol) on a single point and 0.64 (RMSE: 1.80 kcal/mol) on multiple‐point missense mutations across 10‐fold cross‐validation and independent blind tests. For single‐point mutations, DynaMut2 achieved comparable performance with other methods when predicting variations in Gibbs Free Energy (ΔΔG) and in melting temperature (ΔTm). We anticipate our tool to be a valuable suite for the study of protein flexibility analysis and the study of the role of variants in disease. DynaMut2 is freely available as a web server and API at http://biosig.unimelb.edu.au/dynamut2.
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Affiliation(s)
- Carlos H M Rodrigues
- Structural Biology and Bioinformatics, Department of Biochemistry, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia.,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Douglas E V Pires
- Structural Biology and Bioinformatics, Department of Biochemistry, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia.,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.,School of Computing and Information Systems, University of Melbourne, Melbourne, Victoria, Australia
| | - David B Ascher
- Structural Biology and Bioinformatics, Department of Biochemistry, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia.,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.,Department of Biochemistry, University of Cambridge, Cambridge, UK
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Abstract
Mutations in protein-coding regions can lead to large biological changes and are associated with genetic conditions, including cancers and Mendelian diseases, as well as drug resistance. Although whole genome and exome sequencing help to elucidate potential genotype-phenotype correlations, there is a large gap between the identification of new variants and deciphering their molecular consequences. A comprehensive understanding of these mechanistic consequences is crucial to better understand and treat diseases in a more personalized and effective way. This is particularly relevant considering estimates that over 80% of mutations associated with a disease are incorrectly assumed to be causative. A thorough analysis of potential effects of mutations is required to correctly identify the molecular mechanisms of disease and enable the distinction between disease-causing and non-disease-causing variation within a gene. Here we present an overview of our integrative mutation analysis platform, which focuses on refining the current genotype-phenotype correlation methods by using the wealth of protein structural information.
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Novel scaffold hopping of potent benzothiazole and isatin analogues linked to 1,2,3-triazole fragment that mimic quinazoline epidermal growth factor receptor inhibitors: Synthesis, antitumor and mechanistic analyses. Bioorg Chem 2020; 103:104133. [PMID: 32745759 DOI: 10.1016/j.bioorg.2020.104133] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/11/2020] [Accepted: 07/18/2020] [Indexed: 12/13/2022]
Abstract
A series of benzothiazole/isatin linked to 1,2,3-triazole moiety and terminal sulpha drugs 5a-e and 6a-e were synthesized and evaluated for cytotoxic activity against a panel of cancer cell lines. The novel compounds showed variable IC50 range of activity and some of them were potent compared to reference drug. The promising compounds were subjected as postulated the mimicry proposal for quinazoline-based EGFR inhibitors for their inhibitory profile against EGFR TK enzyme. That data obtained revealed that most of these compounds were potent EGFR TK inhibitors at nanomolar concentrations. Among these, compounds 5a and 5b showed more potent activity on EGFR compared to erlotinib (IC50 103 and 104 versus 67.6 nM). Based upon the results, molecular docking analysis was performed on EGFR receptor and proved the strong contribution of fragments; benzothiazole, isatin, and triazole to the binding ATP pocket. When these selected compounds 5a and 5b were tested in an HepG2 model, they could effectively inhibited tumor growth, strongly induced cancer cell apoptosis, and suppressed cell cycle progression leading to DNA fragmentation. Well-DMET profile of the most active derivatives was presented and compared to the reference drugs. Taken together, we introduced novel triazole-sulpha drug hybrid for the first time as EGFR inhibitors and the results of our studies indicate that the newly discovered inhibitors have significant potential for anticancer treatment.
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Pires DEV, Ascher DB. mycoCSM: Using Graph-Based Signatures to Identify Safe Potent Hits against Mycobacteria. J Chem Inf Model 2020; 60:3450-3456. [PMID: 32615035 DOI: 10.1021/acs.jcim.0c00362] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Development of new potent, safe drugs to treat Mycobacteria has proven to be challenging, with limited hit rates of initial screens restricting subsequent development efforts. Despite significant efforts and the evolution of quantitative structure-activity relationship as well as machine learning-based models for computationally predicting molecule bioactivity, there is an unmet need for efficient and reliable methods for identifying biologically active compounds against Mycobacterium that are also safe for humans. Here we developed mycoCSM, a graph-based signature approach to rapidly identify compounds likely to be active against bacteria from the genus Mycobacterium, or against specific Mycobacteria species. mycoCSM was trained and validated on eight organism-specific and for the first time a general Mycobacteria data set, achieving correlation coefficients of up to 0.89 on cross-validation and 0.88 on independent blind tests, when predicting bioactivity in terms of minimum inhibitory concentration. In addition, we also developed a predictor to identify those compounds likely to penetrate in necrotic tuberculosis foci, which achieved a correlation coefficient of 0.75. Together with a built-in estimator of the maximum tolerated dose in humans, we believe this method will provide a valuable resource to enrich screening libraries with potent, safe molecules. To provide simple guidance in the selection of libraries with favorable anti-Mycobacteria properties, we made mycoCSM freely available online at http://biosig.unimelb.edu.au/myco_csm.
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Affiliation(s)
- Douglas E V Pires
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne 3004, VIC, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, 30 Flemington Rd, Parkville 3052, VIC, Australia.,School of Computing and Information Systems, University of Melbourne, Parkville 3052, VIC, Australia
| | - David B Ascher
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne 3004, VIC, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, 30 Flemington Rd, Parkville 3052, VIC, Australia.,Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, England
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Myung Y, Pires DEV, Ascher DB. mmCSM-AB: guiding rational antibody engineering through multiple point mutations. Nucleic Acids Res 2020; 48:W125-W131. [PMID: 32432715 PMCID: PMC7319589 DOI: 10.1093/nar/gkaa389] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/18/2020] [Accepted: 05/16/2020] [Indexed: 12/15/2022] Open
Abstract
While antibodies are becoming an increasingly important therapeutic class, especially in personalized medicine, their development and optimization has been largely through experimental exploration. While there have been many efforts to develop computational tools to guide rational antibody engineering, most approaches are of limited accuracy when applied to antibody design, and have largely been limited to analysing a single point mutation at a time. To overcome this gap, we have curated a dataset of 242 experimentally determined changes in binding affinity upon multiple point mutations in antibody-target complexes (89 increasing and 153 decreasing binding affinity). Here, we have shown that by using our graph-based signatures and atomic interaction information, we can accurately analyse the consequence of multi-point mutations on antigen binding affinity. Our approach outperformed other available tools across cross-validation and two independent blind tests, achieving Pearson's correlations of up to 0.95. We have implemented our new approach, mmCSM-AB, as a web-server that can help guide the process of affinity maturation in antibody design. mmCSM-AB is freely available at http://biosig.unimelb.edu.au/mmcsm_ab/.
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Affiliation(s)
- Yoochan Myung
- Computational Biology and Clinical Informatics, Baker Institute, Melbourne, VIC 3004, Australia
- Structural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, VIC 3052, Australia
| | - Douglas E V Pires
- Computational Biology and Clinical Informatics, Baker Institute, Melbourne, VIC 3004, Australia
- Structural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, VIC 3052, Australia
- School of Computing and Information Systems, University of Melbourne, Parkville, VIC 3052, Australia
| | - David B Ascher
- Computational Biology and Clinical Informatics, Baker Institute, Melbourne, VIC 3004, Australia
- Structural Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, VIC 3052, Australia
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
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Ruan X, Du P, Zhao K, Huang J, Xia H, Dai D, Huang S, Cui X, Liu L, Zhang J. Mechanism of Dayuanyin in the treatment of coronavirus disease 2019 based on network pharmacology and molecular docking. Chin Med 2020; 15:62. [PMID: 32536965 PMCID: PMC7289712 DOI: 10.1186/s13020-020-00346-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/07/2020] [Indexed: 02/07/2023] Open
Abstract
Background At present, coronavirus disease 2019 (COVID-19), caused by infection with severe acute respiratory syndrome coronavirus 2, is spreading all over the world, with disastrous consequences for people of all countries. The traditional Chinese medicine prescription Dayuanyin (DYY), a classic prescription for the treatment of plague, has shown significant effects in the treatment of COVID-19. However, its specific mechanism of action has not yet been clarified. This study aims to explore the mechanism of action of DYY in the treatment of COVID-19 with the hope of providing a theoretical basis for its clinical application. Methods First, the TCMSP database was searched to screen the active ingredients and corresponding target genes of the DYY prescription and to further identify the core compounds in the active ingredient. Simultaneously, the Genecards database was searched to identify targets related to COVID-19. Then, the STRING database was applied to analyse protein–protein interaction, and Cytoscape software was used to draw a network diagram. The R language and DAVID database were used to analyse GO biological processes and KEGG pathway enrichment. Second, AutoDock Vina and other software were used for molecular docking of core targets and core compounds. Finally, before and after application of DYY, the core target gene IL6 of COVID-19 patients was detected by ELISA to validate the clinical effects. Results First, 174 compounds, 7053 target genes of DYY and 251 genes related to COVID-19 were selected, among which there were 45 target genes of DYY associated with treatment of COVID-19. This study demonstrated that the use of DYY in the treatment of COVID-19 involved a variety of biological processes, and DYY acted on key targets such as IL6, ILIB, and CCL2 through signaling pathways such as the IL-17 signaling pathway, AGE-RAGE signaling pathway in diabetic complications, and cytokine–cytokine receptor interaction. DYY might play a vital role in treating COVID-19 by suppressing the inflammatory storm and regulating immune function. Second, the molecular docking results showed that there was a certain affinity between the core compounds (kaempferol, quercetin, 7-Methoxy-2-methyl isoflavone, naringenin, formononetin) and core target genes (IL6, IL1B, CCL2). Finally, clinical studies showed that the level of IL6 was elevated in COVID-19 patients, and DYY can reduce its levels. Conclusions DYY may treat COVID-19 through multiple targets, multiple channels, and multiple pathways and is worthy of clinical application and promotion.
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Affiliation(s)
- Xiaofeng Ruan
- College of Traditional Chinese Medicine, Hubei University of Traditional Chinese Medicine, Wuhan, 430070 China.,Department of Liver Medicine, Hubei NO.3 People's Hospital of Jianghan University, Wuhan, 430033 China
| | - Peng Du
- Department of Rehabilitation Medicine, Xiangyang Central Hospital, Xiangyang, 441021 Hubei China
| | - Kang Zhao
- Department of Liver Medicine, Hubei NO.3 People's Hospital of Jianghan University, Wuhan, 430033 China
| | - Jucun Huang
- Department of Liver Medicine, Hubei NO.3 People's Hospital of Jianghan University, Wuhan, 430033 China
| | - Hongmei Xia
- Department of Liver Medicine, Hubei NO.3 People's Hospital of Jianghan University, Wuhan, 430033 China
| | - Dan Dai
- Department of Liver Medicine, Hubei NO.3 People's Hospital of Jianghan University, Wuhan, 430033 China
| | - Shu Huang
- Department of Liver Medicine, Hubei NO.3 People's Hospital of Jianghan University, Wuhan, 430033 China
| | - Xiang Cui
- Department of Liver Medicine, AnKang Hospital of Traditional Chinese Medicine, Ankang, 72500 Shaanxi China
| | - Liming Liu
- College of Traditional Chinese Medicine, Hubei University of Traditional Chinese Medicine, Wuhan, 430070 China.,Department of Liver Medicine, Hubei NO.3 People's Hospital of Jianghan University, Wuhan, 430033 China
| | - Jianjun Zhang
- College of Traditional Chinese Medicine, Hubei University of Traditional Chinese Medicine, Wuhan, 430070 China.,Department of Liver Medicine, Hubei NO.3 People's Hospital of Jianghan University, Wuhan, 430033 China
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Novel molecular discovery of promising amidine-based thiazole analogues as potent dual Matrix Metalloproteinase-2 and 9 inhibitors: Anticancer activity data with prominent cell cycle arrest and DNA fragmentation analysis effects. Bioorg Chem 2020; 101:103992. [PMID: 32554279 DOI: 10.1016/j.bioorg.2020.103992] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/20/2020] [Accepted: 05/30/2020] [Indexed: 12/18/2022]
Abstract
Thiazole derivatives are known to possess various biological activities such as antiparasitic, antifungal, antimicrobial and antiproliferative activities. Matrix metalloproteinases (MMPs) are important protease target involved in tumor progression including angiogenesis, tissue invasion, and migration. Therefore, MMPs have also been reported as potential diagnostic and prognostic biomarkers in many types of cancer. Herein, new aryl thiazoles were synthesized and evaluated for their anticancer effects on a panel of cancer cell lines including the invasive MDA-MB-231 line. Some of these compounds showed IC50 values in the submicromolar range in anti-proliferative assays. In order to examine the relationship between their anticancer activity and MMPs targets, the compounds were evaluated for their inhibitory effects on MMP-2 and 9. That data obtained revealed that most of these compounds were potent dual MMP-2/9 inhibitors at nanomolar concentrations. Among these, 2-(1-(2-(2-((E)-4-iodobenzylidene)hydrazineyl)-4-methylthiazol-5-yl)ethylidene)hydrazine-1-carboximidamide (4a) was the most potent non-selective dual MMP-2/9 inhibitor with inhibitory concentrations of 56 and 38 nM respectively. When compound 4a was tested in an MDA-MB-231, HCT-116, MCF-7 model, it effectively inhibited tumor growth, strongly induced cancer cell apoptosis, inhibit cell migration, and suppressed cell cycle progression leading to DNA fragmentation. Taken together, the results of our studies indicate that the newly discovered thiazole-based MMP-2/9 inhibitors have significant potential for anticancer treatment.
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The rational design, synthesis, and antimicrobial investigation of 2-Amino-4-Methylthiazole analogues inhibitors of GlcN-6-P synthase. Bioorg Chem 2020; 99:103781. [DOI: 10.1016/j.bioorg.2020.103781] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/15/2020] [Accepted: 03/19/2020] [Indexed: 12/21/2022]
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45
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Vangone A, Schaarschmidt J, Koukos P, Geng C, Citro N, Trellet ME, Xue LC, Bonvin AMJJ. Large-scale prediction of binding affinity in protein-small ligand complexes: the PRODIGY-LIG web server. Bioinformatics 2020; 35:1585-1587. [PMID: 31051038 DOI: 10.1093/bioinformatics/bty816] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 08/15/2018] [Accepted: 09/19/2018] [Indexed: 11/14/2022] Open
Abstract
SUMMARY Recently we published PROtein binDIng enerGY (PRODIGY), a web-server for the prediction of binding affinity in protein-protein complexes. By using a combination of simple structural properties, such as the residue-contacts made at the interface, PRODIGY has demonstrated a top performance compared with other state-of-the-art predictors in the literature. Here we present an extension of it, named PRODIGY-LIG, aimed at the prediction of affinity in protein-small ligand complexes. The predictive method, properly readapted for small ligand by making use of atomic instead of residue contacts, has been successfully applied for the blind prediction of 102 protein-ligand complexes during the D3R Grand Challenge 2. PRODIGY-LIG has the advantage of being simple, generic and applicable to any kind of protein-ligand complex. It provides an automatic, fast and user-friendly tool ensuring broad accessibility. AVAILABILITY AND IMPLEMENTATION PRODIGY-LIG is freely available without registration requirements at http://milou.science.uu.nl/services/PRODIGY-LIG.
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Affiliation(s)
- Anna Vangone
- Department of Chemistry, Faculty of Science, Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht, The Netherlands
| | - Joerg Schaarschmidt
- Department of Chemistry, Faculty of Science, Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht, The Netherlands
| | - Panagiotis Koukos
- Department of Chemistry, Faculty of Science, Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht, The Netherlands
| | - Cunliang Geng
- Department of Chemistry, Faculty of Science, Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht, The Netherlands
| | - Nevia Citro
- Department of Chemistry, Faculty of Science, Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht, The Netherlands
| | - Mikael E Trellet
- Department of Chemistry, Faculty of Science, Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht, The Netherlands
| | - Li C Xue
- Department of Chemistry, Faculty of Science, Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht, The Netherlands
| | - Alexandre M J J Bonvin
- Department of Chemistry, Faculty of Science, Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht, The Netherlands
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Kumar M, Martin A, Nirgude S, Chaudhary B, Mondal S, Sarkar A. Quinacrine inhibits GSTA1 activity and induces apoptosis through G 1/S arrest and generation of ROS in human non-small cell lung cancer cell lines. Oncotarget 2020; 11:1603-1617. [PMID: 32405336 PMCID: PMC7210017 DOI: 10.18632/oncotarget.27558] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 12/02/2019] [Indexed: 01/09/2023] Open
Abstract
Background: Quinacrine (QC) is popular for its anti-malarial activity. It has been reported exhibiting anti-cancerous properties by suppressing nuclear factor-κB and activating p53 signaling; however, its effect on cellular pathways in human non-small cell lung cancer (NSCLC) has not been studied. Materials and Methods: Binding of QC with GSTA1 was studied computationally as well as through GST activity assay kit. Cell viability, cell cycle and mitochondrial membrane potential activity were studied using flow cytometry. RT-PCR and western blot were carried out to understand the involvement of various genes at their mRNA as well as protein level. Results: QC inhibited the activity of GSTA1 approximately by 40–45% which inhibits cell survival and promotes apoptosis. QC reduced viability of NSCLC cells in a dose-dependent manner. It also causes nuclear fragmentation, G1/S arrest of cell cycle and ROS generation; which along with disruption of mitochondrial membrane potential activity leads to apoptotic fate. Conclusions: Results revealed, QC has promising anti-cancer potential against NSCLC cells via inhibition of GSTA1, induction of G1/S arrest and ROS mediated apoptotic signaling.
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Affiliation(s)
- Makhan Kumar
- CMBL, Department of Biological Sciences, CMBL, BITS Pilani K K Birla Goa Campus, Zuarinagar, Goa 40372, India
| | - Ansie Martin
- CMBL, Department of Biological Sciences, CMBL, BITS Pilani K K Birla Goa Campus, Zuarinagar, Goa 40372, India.,Present Address: UMR 1236, Faculty of Medicine, Rennes 35043, France
| | - Snehal Nirgude
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bangalore, Electronics City Phase 1, Bengaluru, Karnataka 560100, India.,Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Bibha Chaudhary
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bangalore, Electronics City Phase 1, Bengaluru, Karnataka 560100, India
| | - Sukanta Mondal
- CMBL, Department of Biological Sciences, CMBL, BITS Pilani K K Birla Goa Campus, Zuarinagar, Goa 40372, India
| | - Angshuman Sarkar
- CMBL, Department of Biological Sciences, CMBL, BITS Pilani K K Birla Goa Campus, Zuarinagar, Goa 40372, India
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Singh N, Chaput L, Villoutreix BO. Virtual screening web servers: designing chemical probes and drug candidates in the cyberspace. Brief Bioinform 2020; 22:1790-1818. [PMID: 32187356 PMCID: PMC7986591 DOI: 10.1093/bib/bbaa034] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The interplay between life sciences and advancing technology drives a continuous cycle of chemical data growth; these data are most often stored in open or partially open databases. In parallel, many different types of algorithms are being developed to manipulate these chemical objects and associated bioactivity data. Virtual screening methods are among the most popular computational approaches in pharmaceutical research. Today, user-friendly web-based tools are available to help scientists perform virtual screening experiments. This article provides an overview of internet resources enabling and supporting chemical biology and early drug discovery with a main emphasis on web servers dedicated to virtual ligand screening and small-molecule docking. This survey first introduces some key concepts and then presents recent and easily accessible virtual screening and related target-fishing tools as well as briefly discusses case studies enabled by some of these web services. Notwithstanding further improvements, already available web-based tools not only contribute to the design of bioactive molecules and assist drug repositioning but also help to generate new ideas and explore different hypotheses in a timely fashion while contributing to teaching in the field of drug development.
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Affiliation(s)
- Natesh Singh
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Ludovic Chaput
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Bruno O Villoutreix
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 Drugs and Molecules for Living Systems, F-59000 Lille, France
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Ramsbottom KA, Carr DF, Rigden DJ, Jones AR. Informatics investigations into anti-thyroid drug induced agranulocytosis associated with multiple HLA-B alleles. PLoS One 2020; 15:e0220754. [PMID: 32027661 PMCID: PMC7004376 DOI: 10.1371/journal.pone.0220754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 01/22/2020] [Indexed: 11/18/2022] Open
Abstract
INTRODUCTION Adverse drug reactions have been linked with HLA alleles in different studies. These HLA proteins play an essential role in the adaptive immune response for the presentation of self and non-self peptides. Anti-thyroid drugs methimazole and propylthiouracil have been associated with drug induced agranulocytosis (severe lower white blood cell count) in patients with B*27:05, B*38:02 and DRB1*08:03 alleles in different populations: Taiwanese, Vietnamese, Han Chinese and Caucasian. METHODS In this study, informatics methods were used to investigate if any sequence or structural similarities exist between the two associated HLA-B alleles, compared with a set of "control" alleles assumed not be associated, which could help explain the molecular basis of the adverse drug reaction. We demonstrated using MHC Motif Viewer and MHCcluster that the two alleles do not have a propensity to bind similar peptides, and thus at a gross level the structure of the antigen presentation region of the two alleles are not similar. We also performed multiple sequence alignment to identify polymorphisms shared by the risk but not by the control alleles and molecular docking to compare the predicted binding poses of the drug-allele combinations. RESULTS Two residues, Cys67 and Thr80, were identified from the multiple sequence alignments to be unique to these risk alleles alone. The molecular docking showed the poses of the risk alleles to favour the F-pocket of the peptide binding groove, close to the Thr80 residue, with the control alleles generally favouring a different pocket. The data are thus suggestive that Thr80 may be a critical residue in HLA-mediated anti-thyroid drug induced agranulocytosis, and thus can guide future research and risk assessment.
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Affiliation(s)
- Kerry A. Ramsbottom
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Daniel F. Carr
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Daniel J. Rigden
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Andrew R. Jones
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- * E-mail:
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Li H, Sze K, Lu G, Ballester PJ. Machine‐learning scoring functions for structure‐based drug lead optimization. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1465] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Hongjian Li
- CUHK‐SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences Chinese University of Hong Kong Shatin Hong Kong
| | - Kam‐Heung Sze
- CUHK‐SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences Chinese University of Hong Kong Shatin Hong Kong
| | - Gang Lu
- CUHK‐SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences Chinese University of Hong Kong Shatin Hong Kong
| | - Pedro J. Ballester
- Cancer Research Center of Marseille (INSERM U1068, Institut Paoli‐Calmettes, Aix‐Marseille Université UM105, CNRS UMR7258) Marseille France
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50
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Karmakar M, Rodrigues CHM, Horan K, Denholm JT, Ascher DB. Structure guided prediction of Pyrazinamide resistance mutations in pncA. Sci Rep 2020; 10:1875. [PMID: 32024884 PMCID: PMC7002382 DOI: 10.1038/s41598-020-58635-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/28/2019] [Indexed: 11/29/2022] Open
Abstract
Pyrazinamide plays an important role in tuberculosis treatment; however, its use is complicated by side-effects and challenges with reliable drug susceptibility testing. Resistance to pyrazinamide is largely driven by mutations in pyrazinamidase (pncA), responsible for drug activation, but genetic heterogeneity has hindered development of a molecular diagnostic test. We proposed to use information on how variants were likely to affect the 3D structure of pncA to identify variants likely to lead to pyrazinamide resistance. We curated 610 pncA mutations with high confidence experimental and clinical information on pyrazinamide susceptibility. The molecular consequences of each mutation on protein stability, conformation, and interactions were computationally assessed using our comprehensive suite of graph-based signature methods, mCSM. The molecular consequences of the variants were used to train a classifier with an accuracy of 80%. Our model was tested against internationally curated clinical datasets, achieving up to 85% accuracy. Screening of 600 Victorian clinical isolates identified a set of previously unreported variants, which our model had a 71% agreement with drug susceptibility testing. Here, we have shown the 3D structure of pncA can be used to accurately identify pyrazinamide resistance mutations. SUSPECT-PZA is freely available at: http://biosig.unimelb.edu.au/suspect_pza/.
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Affiliation(s)
- Malancha Karmakar
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
- Victorian Tuberculosis Program, Melbourne Health and Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Carlos H M Rodrigues
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Kristy Horan
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at The Peter Doherty Institute for Infection &Immunity, Melbourne, Victoria, Australia
| | - Justin T Denholm
- Victorian Tuberculosis Program, Melbourne Health and Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - David B Ascher
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia.
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.
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