1
|
Zhu Y, Gu J, Zhao Z, Chan AWE, Mojica MF, Hujer AM, Bonomo RA, Haider S. Deciphering the Coevolutionary Dynamics of L2 β-Lactamases via Deep Learning. J Chem Inf Model 2024; 64:3706-3717. [PMID: 38687957 PMCID: PMC11094718 DOI: 10.1021/acs.jcim.4c00189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/10/2024] [Accepted: 04/09/2024] [Indexed: 05/02/2024]
Abstract
L2 β-lactamases, serine-based class A β-lactamases expressed by Stenotrophomonas maltophilia, play a pivotal role in antimicrobial resistance (AMR). However, limited studies have been conducted on these important enzymes. To understand the coevolutionary dynamics of L2 β-lactamase, innovative computational methodologies, including adaptive sampling molecular dynamics simulations, and deep learning methods (convolutional variational autoencoders and BindSiteS-CNN) explored conformational changes and correlations within the L2 β-lactamase family together with other representative class A enzymes including SME-1 and KPC-2. This work also investigated the potential role of hydrophobic nodes and binding site residues in facilitating the functional mechanisms. The convergence of analytical approaches utilized in this effort yielded comprehensive insights into the dynamic behavior of the β-lactamases, specifically from an evolutionary standpoint. In addition, this analysis presents a promising approach for understanding how the class A β-lactamases evolve in response to environmental pressure and establishes a theoretical foundation for forthcoming endeavors in drug development aimed at combating AMR.
Collapse
Affiliation(s)
- Yu Zhu
- Pharmaceutical
and Biological Chemistry, UCL School of
Pharmacy, London WC1N 1AX, U.K.
| | - Jing Gu
- Pharmaceutical
and Biological Chemistry, UCL School of
Pharmacy, London WC1N 1AX, U.K.
| | - Zhuoran Zhao
- Pharmaceutical
and Biological Chemistry, UCL School of
Pharmacy, London WC1N 1AX, U.K.
| | - A. W. Edith Chan
- Division
of Medicine, UCL School of Pharmacy, London WC1E 6BT, U.K.
| | - Maria F. Mojica
- Department
of Molecular Biology and Microbiology, Case
Western Reserve University School of Medicine, Cleveland, Ohio 44106-5029, United
States
- Research
Service, Department of Veterans Affairs Medical Center, Louis Stokes Cleveland, Cleveland, Ohio 44106-1702, United States
- CWRU-Cleveland
VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA
CARES), Cleveland, Ohio 44106-5029, United States
| | - Andrea M. Hujer
- Research
Service, Department of Veterans Affairs Medical Center, Louis Stokes Cleveland, Cleveland, Ohio 44106-1702, United States
- Department
of Medicine, Case Western Reserve University
School of Medicine, Cleveland, Ohio 44106-5029, United States
| | - Robert A. Bonomo
- Research
Service, Department of Veterans Affairs Medical Center, Louis Stokes Cleveland, Cleveland, Ohio 44106-1702, United States
- CWRU-Cleveland
VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA
CARES), Cleveland, Ohio 44106-5029, United States
- Clinician
Scientist Investigator, Department of Veterans Affairs Medical Center, Louis Stokes Cleveland, Cleveland, Ohio 44106-1702, United States
- Departments
of Pharmacology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106-5029, United
States
- Departments
of Molecular Biology and Microbiology, Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106-5029, United
States
| | - Shozeb Haider
- Pharmaceutical
and Biological Chemistry, UCL School of
Pharmacy, London WC1N 1AX, U.K.
- UCL
Centre for Advanced Research in Computing, University College London, London WC1H 9RL, U.K.
| |
Collapse
|
2
|
Ryan E, Nishimura S, Lopez G, Tayebi N, Sidransky E. Phenotypic consequences of GBA1 pathological variant R463C (p.R502C). Am J Med Genet A 2024:e63630. [PMID: 38647370 DOI: 10.1002/ajmg.a.63630] [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: 03/07/2024] [Revised: 03/22/2024] [Accepted: 03/31/2024] [Indexed: 04/25/2024]
Abstract
Gaucher disease (GD) is an autosomal recessively inherited lysosomal storage disorder caused by biallelic pathological variants in the GBA1 gene. Patients present along a broad clinical spectrum, and phenotypes are often difficult to predict based on genotype alone. The variant R463C (p.Arg502Cys) exemplifies this challenge. To better characterize its different clinical presentations, we examined the records of 25 current and historical patients evaluated at the National Institutes of Health. Nine patients were classified as GD1, 14 were classified as GD3, and two had an ambiguous diagnosis between GD1 and GD3. In addition, we reviewed the published literature in PubMed and Web of Science through December 2023, identifying 62 cases with an R463C variant from 18 countries. Within the NIH cohort, the most common second variants were N370S (p.N409S) and L444P (p.L483P). R463C/L444P was encountered in patients with GD1 and GD3 in both the NIH cohort and worldwide. In the literature, R463C/R463C was also reported in both GD1 and GD3, although sparse phenotypic information was shared. Often the phenotype reflected what might be predicted for the second mutant allele. This diversity of phenotypes emphasizes the need for longitudinal follow-up to assess symptom development and neurological involvement.
Collapse
Affiliation(s)
- Emory Ryan
- National Human Genome Research Institute, National Institutes of Health, Bethesda, USA
| | - Samantha Nishimura
- National Human Genome Research Institute, National Institutes of Health, Bethesda, USA
| | - Grisel Lopez
- National Human Genome Research Institute, National Institutes of Health, Bethesda, USA
| | - Nahid Tayebi
- National Human Genome Research Institute, National Institutes of Health, Bethesda, USA
| | - Ellen Sidransky
- National Human Genome Research Institute, National Institutes of Health, Bethesda, USA
| |
Collapse
|
3
|
Gehrlein A, Udayar V, Anastasi N, Morella ML, Ruf I, Brugger D, von der Mark S, Thoma R, Rufer A, Heer D, Pfahler N, Jochner A, Niewoehner J, Wolf L, Fueth M, Ebeling M, Villaseñor R, Zhu Y, Deen MC, Shan X, Ehsaei Z, Taylor V, Sidransky E, Vocadlo DJ, Freskgård PO, Jagasia R. Targeting neuronal lysosomal dysfunction caused by β-glucocerebrosidase deficiency with an enzyme-based brain shuttle construct. Nat Commun 2023; 14:2057. [PMID: 37045813 PMCID: PMC10097658 DOI: 10.1038/s41467-023-37632-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 03/24/2023] [Indexed: 04/14/2023] Open
Abstract
Mutations in glucocerebrosidase cause the lysosomal storage disorder Gaucher's disease and are the most common risk factor for Parkinson's disease. Therapies to restore the enzyme's function in the brain hold great promise for treating the neurological implications. Thus, we developed blood-brain barrier penetrant therapeutic molecules by fusing transferrin receptor-binding moieties to β-glucocerebrosidase (referred to as GCase-BS). We demonstrate that these fusion proteins show significantly increased uptake and lysosomal efficiency compared to the enzyme alone. In a cellular disease model, GCase-BS rapidly rescues the lysosomal proteome and lipid accumulations beyond known substrates. In a mouse disease model, intravenous injection of GCase-BS leads to a sustained reduction of glucosylsphingosine and can lower neurofilament-light chain plasma levels. Collectively, these findings demonstrate the potential of GCase-BS for treating GBA1-associated lysosomal dysfunction, provide insight into candidate biomarkers, and may ultimately open a promising treatment paradigm for lysosomal storage diseases extending beyond the central nervous system.
Collapse
Affiliation(s)
- Alexandra Gehrlein
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases Discovery and Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland.
| | - Vinod Udayar
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases Discovery and Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Nadia Anastasi
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases Discovery and Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Martino L Morella
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases Discovery and Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
- Department of Anatomy and Neurosciences, Amsterdam University Medical Center | VUmc, Amsterdam, Netherlands
| | - Iris Ruf
- Roche Pharma Research and Early Development, Therapeutic Modalities, Lead Discovery, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Doris Brugger
- Roche Pharma Research and Early Development, Therapeutic Modalities, Lead Discovery, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Sophia von der Mark
- Roche Pharma Research and Early Development, Therapeutic Modalities, Lead Discovery, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Ralf Thoma
- Roche Pharma Research and Early Development, Therapeutic Modalities, Lead Discovery, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Arne Rufer
- Roche Pharma Research and Early Development, Therapeutic Modalities, Lead Discovery, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Dominik Heer
- Roche Pharma Research and Early Development, Therapeutic Modalities, Lead Discovery, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Nina Pfahler
- Roche Pharma Research and Early Development, Therapeutic Modalities, Lead Discovery, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
- Interfaculty Institute of Biochemistry & Structural Biology Biochemistry (IFIB), Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Anton Jochner
- Roche Pharma Research and Early Development, Therapeutic Modalities Large Molecule Research, Roche Innovation Center Munich, Roche Diagnostics GmbH, Penzberg, Germany
| | - Jens Niewoehner
- Roche Pharma Research and Early Development, Therapeutic Modalities Large Molecule Research, Roche Innovation Center Munich, Roche Diagnostics GmbH, Penzberg, Germany
| | - Luise Wolf
- Roche Pharma Research and Early Development, Data & Analytics, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Matthias Fueth
- Roche Pharma Research and Early Development, Pharmaceutical Science, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Martin Ebeling
- Roche Pharma Research and Early Development, Pharmaceutical Science, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Roberto Villaseñor
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases Discovery and Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Yanping Zhu
- Department of Chemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Matthew C Deen
- Department of Chemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Xiaoyang Shan
- Department of Chemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Zahra Ehsaei
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Verdon Taylor
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Ellen Sidransky
- Molecular Neurogenetics Section, National Human Genome Research Institute, Bethesda, MD, USA
| | - David J Vocadlo
- Department of Chemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Per-Ola Freskgård
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases Discovery and Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
- BioArctic AB, Stockholm, Sweden
| | - Ravi Jagasia
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases Discovery and Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland.
| |
Collapse
|
4
|
Zhao Z, Shen X, Chen S, Gu J, Wang H, Mojica MF, Samanta M, Bhowmik D, Vila AJ, Bonomo RA, Haider S. Gating interactions steer loop conformational changes in the active site of the L1 metallo-β-lactamase. eLife 2023; 12:e83928. [PMID: 36826989 PMCID: PMC9977270 DOI: 10.7554/elife.83928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 02/03/2023] [Indexed: 02/25/2023] Open
Abstract
β-Lactam antibiotics are the most important and widely used antibacterial agents across the world. However, the widespread dissemination of β-lactamases among pathogenic bacteria limits the efficacy of β-lactam antibiotics. This has created a major public health crisis. The use of β-lactamase inhibitors has proven useful in restoring the activity of β-lactam antibiotics, yet, effective clinically approved inhibitors against class B metallo-β-lactamases are not available. L1, a class B3 enzyme expressed by Stenotrophomonas maltophilia, is a significant contributor to the β-lactam resistance displayed by this opportunistic pathogen. Structurally, L1 is a tetramer with two elongated loops, α3-β7 and β12-α5, present around the active site of each monomer. Residues in these two loops influence substrate/inhibitor binding. To study how the conformational changes of the elongated loops affect the active site in each monomer, enhanced sampling molecular dynamics simulations were performed, Markov State Models were built, and convolutional variational autoencoder-based deep learning was applied. The key identified residues (D150a, H151, P225, Y227, and R236) were mutated and the activity of the generated L1 variants was evaluated in cell-based experiments. The results demonstrate that there are extremely significant gating interactions between α3-β7 and β12-α5 loops. Taken together, the gating interactions with the conformational changes of the key residues play an important role in the structural remodeling of the active site. These observations offer insights into the potential for novel drug development exploiting these gating interactions.
Collapse
Affiliation(s)
- Zhuoran Zhao
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
| | - Xiayu Shen
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
| | - Shuang Chen
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
| | - Jing Gu
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
| | - Haun Wang
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
| | - Maria F Mojica
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of MedicineClevelandUnited States
- Louis Stokes Cleveland Department of Veterans Affairs Medical CenterClevelandUnited States
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES)ClevelandUnited States
| | - Moumita Samanta
- College of Computing, Georgia Institute of TechnologyAtlantaUnited States
| | - Debsindhu Bhowmik
- Computer Science and Engineering Division, Oak Ridge National LaboratoriesOak RidgeUnited States
| | - Alejandro J Vila
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES)ClevelandUnited States
- Laboratorio de Metaloproteínas, Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR)RosarioArgentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de RosarioRosarioArgentina
| | - Robert A Bonomo
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of MedicineClevelandUnited States
- Louis Stokes Cleveland Department of Veterans Affairs Medical CenterClevelandUnited States
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES)ClevelandUnited States
- Departments of Medicine, Biochemistry, Pharmacology, and Proteomics and Bioinformatics, Case Western Reserve University School of MedicineClevelandUnited States
| | - Shozeb Haider
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
- UCL Centre for Advanced Research Computing, University College LondonLondonUnited Kingdom
| |
Collapse
|
5
|
Lee J, Liu C, Kim J, Chen Z, Sun Y, Rogers JR, Chung WK, Weng C. Deep learning for rare disease: A scoping review. J Biomed Inform 2022; 135:104227. [DOI: 10.1016/j.jbi.2022.104227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/22/2022] [Accepted: 10/07/2022] [Indexed: 10/31/2022]
|
6
|
Protein Function Analysis through Machine Learning. Biomolecules 2022; 12:biom12091246. [PMID: 36139085 PMCID: PMC9496392 DOI: 10.3390/biom12091246] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/22/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
Machine learning (ML) has been an important arsenal in computational biology used to elucidate protein function for decades. With the recent burgeoning of novel ML methods and applications, new ML approaches have been incorporated into many areas of computational biology dealing with protein function. We examine how ML has been integrated into a wide range of computational models to improve prediction accuracy and gain a better understanding of protein function. The applications discussed are protein structure prediction, protein engineering using sequence modifications to achieve stability and druggability characteristics, molecular docking in terms of protein–ligand binding, including allosteric effects, protein–protein interactions and protein-centric drug discovery. To quantify the mechanisms underlying protein function, a holistic approach that takes structure, flexibility, stability, and dynamics into account is required, as these aspects become inseparable through their interdependence. Another key component of protein function is conformational dynamics, which often manifest as protein kinetics. Computational methods that use ML to generate representative conformational ensembles and quantify differences in conformational ensembles important for function are included in this review. Future opportunities are highlighted for each of these topics.
Collapse
|
7
|
Esfandiary A, Finkelstein DI, Voelcker NH, Rudd D. Clinical Sphingolipids Pathway in Parkinson’s Disease: From GCase to Integrated-Biomarker Discovery. Cells 2022; 11:cells11081353. [PMID: 35456032 PMCID: PMC9028315 DOI: 10.3390/cells11081353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 02/01/2023] Open
Abstract
Alterations in the sphingolipid metabolism of Parkinson’s Disease (PD) could be a potential diagnostic feature. Only around 10–15% of PD cases can be diagnosed through genetic alterations, while the remaining population, idiopathic PD (iPD), manifest without validated and specific biomarkers either before or after motor symptoms appear. Therefore, clinical diagnosis is reliant on the skills of the clinician, which can lead to misdiagnosis. IPD cases present with a spectrum of non-specific symptoms (e.g., constipation and loss of the sense of smell) that can occur up to 20 years before motor function loss (prodromal stage) and formal clinical diagnosis. Prodromal alterations in metabolites and proteins from the pathways underlying these symptoms could act as biomarkers if they could be differentiated from the broad values seen in a healthy age-matched control population. Additionally, these shifts in metabolites could be integrated with other emerging biomarkers/diagnostic tests to give a PD-specific signature. Here we provide an up-to-date review of the diagnostic value of the alterations in sphingolipids pathway in PD by focusing on the changes in definitive PD (postmortem confirmed brain data) and their representation in “probable PD” cerebrospinal fluid (CSF) and blood. We conclude that the trend of holistic changes in the sphingolipid pathway in the PD brain seems partly consistent in CSF and blood, and could be one of the most promising pathways in differentiating PD cases from healthy controls, with the potential to improve early-stage iPD diagnosis and distinguish iPD from other Parkinsonism when combined with other pathological markers.
Collapse
Affiliation(s)
- Ali Esfandiary
- Drug Delivery, Disposition and Dynamics, Monash University, Parkville, VIC 3052, Australia; (A.E.); (N.H.V.)
- Melbourne Centre for Nanofabrication, Victorian Node of the Australian National Fabrication Facility, Clayton, VIC 3168, Australia
| | | | - Nicolas Hans Voelcker
- Drug Delivery, Disposition and Dynamics, Monash University, Parkville, VIC 3052, Australia; (A.E.); (N.H.V.)
- Melbourne Centre for Nanofabrication, Victorian Node of the Australian National Fabrication Facility, Clayton, VIC 3168, Australia
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Clayton, VIC 3168, Australia
- Materials Science and Engineering, Monash University, Clayton, VIC 3168, Australia
| | - David Rudd
- Drug Delivery, Disposition and Dynamics, Monash University, Parkville, VIC 3052, Australia; (A.E.); (N.H.V.)
- Melbourne Centre for Nanofabrication, Victorian Node of the Australian National Fabrication Facility, Clayton, VIC 3168, Australia
- Correspondence: ; Tel.: +61-3-9903-9581
| |
Collapse
|
8
|
Ose NJ, Butler BM, Kumar A, Kazan IC, Sanderford M, Kumar S, Ozkan SB. Dynamic coupling of residues within proteins as a mechanistic foundation of many enigmatic pathogenic missense variants. PLoS Comput Biol 2022; 18:e1010006. [PMID: 35389981 PMCID: PMC9017885 DOI: 10.1371/journal.pcbi.1010006] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 04/19/2022] [Accepted: 03/09/2022] [Indexed: 01/07/2023] Open
Abstract
Many pathogenic missense mutations are found in protein positions that are neither well-conserved nor fall in any known functional domains. Consequently, we lack any mechanistic underpinning of dysfunction caused by such mutations. We explored the disruption of allosteric dynamic coupling between these positions and the known functional sites as a possible mechanism for pathogenesis. In this study, we present an analysis of 591 pathogenic missense variants in 144 human enzymes that suggests that allosteric dynamic coupling of mutated positions with known active sites is a plausible biophysical mechanism and evidence of their functional importance. We illustrate this mechanism in a case study of β-Glucocerebrosidase (GCase) in which a vast majority of 94 sites harboring Gaucher disease-associated missense variants are located some distance away from the active site. An analysis of the conformational dynamics of GCase suggests that mutations on these distal sites cause changes in the flexibility of active site residues despite their distance, indicating a dynamic communication network throughout the protein. The disruption of the long-distance dynamic coupling caused by missense mutations may provide a plausible general mechanistic explanation for biological dysfunction and disease.
Collapse
Affiliation(s)
- Nicholas J. Ose
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, United States of America
| | - Brandon M. Butler
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, United States of America
| | - Avishek Kumar
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, United States of America
| | - I. Can Kazan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, United States of America
| | - Maxwell Sanderford
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
- Center for Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - S. Banu Ozkan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, United States of America
| |
Collapse
|
9
|
Petese A, Cesaroni V, Cerri S, Blandini F. Are Lysosomes Potential Therapeutic Targets for Parkinson's Disease? CNS & NEUROLOGICAL DISORDERS DRUG TARGETS 2022; 21:642-655. [PMID: 34370650 DOI: 10.2174/1871527320666210809123630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/16/2021] [Accepted: 06/10/2021] [Indexed: 06/13/2023]
Abstract
Parkinson´s Disease (PD) is the second most common neurodegenerative disorder, affecting ~2-3% of the population over 65 years old. In addition to progressive degeneration of nigrostriatal neurons, the histopathological feature of PD is the accumulation of misfolded α-synuclein protein in abnormal cytoplasmatic inclusions, known as Lewy Bodies (LBs). Recently, Genome-Wide Association Studies (GWAS) have indicated a clear association of variants within several lysosomal genes with risk for PD. Newly evolving data have been shedding light on the relationship between lysosomal dysfunction and alpha-synuclein aggregation. Defects in lysosomal enzymes could lead to the insufficient clearance of neurotoxic protein materials, possibly leading to selective degeneration of dopaminergic neurons. Specific modulation of lysosomal pathways and their components could be considered a novel opportunity for therapeutic intervention for PD. The purpose of this review is to illustrate lysosomal biology and describe the role of lysosomal dysfunction in PD pathogenesis. Finally, the most promising novel therapeutic approaches designed to modulate lysosomal activity, as a potential disease-modifying treatment for PD will be highlighted.
Collapse
Affiliation(s)
- Alessandro Petese
- Cellular and Molecular Neurobiology Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Valentina Cesaroni
- Cellular and Molecular Neurobiology Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Silvia Cerri
- Cellular and Molecular Neurobiology Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Fabio Blandini
- Cellular and Molecular Neurobiology Unit, IRCCS Mondino Foundation, Pavia, Italy
- Department of Brain and Behavioural Sciences, University of Pavia, Pavia, Italy
| |
Collapse
|
10
|
Mehendale N, Mallik R, Kamat SS. Mapping Sphingolipid Metabolism Pathways during Phagosomal Maturation. ACS Chem Biol 2021; 16:2757-2765. [PMID: 34647453 DOI: 10.1021/acschembio.1c00393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phagocytosis is an important physiological process, which, in higher organisms, is a means of fighting infections and clearing cellular debris. During phagocytosis, detrimental foreign particles (e.g. pathogens and apoptotic cells) are engulfed by phagocytes (e.g. macrophages), enclosed in membrane-bound vesicles called phagosomes, and transported to the lysosome for eventual detoxification. During this well-choreographed process, the nascent phagosome (also called early phagosome, EP) undergoes a series of spatiotemporally regulated changes in its protein and lipid composition and matures into a late phagosome (LP), which subsequently fuses with the lysosomal membrane to form the phagolysosome. While several elegant proteomic studies have identified the role of unique proteins during phagosomal maturation, the corresponding lipidomic studies are sparse. Recently, we reported a comparative lipidomic analysis between EPs and LPs and showed that ceramides are enriched on the LPs. Further, we found that this ceramide accumulation on LPs was orchestrated by ceramide synthase 2, inhibition of which hampers phagosomal maturation. Following up on this study, here, using biochemical assays, we first show that the increased ceramidase activity on EPs also significantly contributes to the accumulation of ceramides on LPs. Next, leveraging lipidomics, we show that de novo ceramide synthesis does not significantly contribute to the ceramide accumulation on LPs, while concomitant to increased ceramides, glucosylceramides are substantially elevated on LPs. We validate this interesting finding using biochemical assays and show that LPs indeed have heightened glucosylceramide synthase activity. Taken together, our studies provide interesting insights and possible new roles of sphingolipid metabolism during phagosomal maturation.
Collapse
Affiliation(s)
- Neelay Mehendale
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Roop Mallik
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Powai, Mumbai 400076, India
| | - Siddhesh S. Kamat
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| |
Collapse
|
11
|
Bux K, Shen X, Tariq M, Yin J, Moin ST, Bhowmik D, Haider S. Inter-Subunit Dynamics Controls Tunnel Formation During the Oxygenation Process in Hemocyanin Hexamers. Front Mol Biosci 2021; 8:710623. [PMID: 34604302 PMCID: PMC8479113 DOI: 10.3389/fmolb.2021.710623] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 08/23/2021] [Indexed: 11/13/2022] Open
Abstract
Hemocyanin from horseshoe crab in its active form is a homo-hexameric protein. It exists in open and closed conformations when transitioning between deoxygenated and oxygenated states. Here, we present a detailed dynamic atomistic investigation of the oxygenated and deoxygenated states of the hexameric hemocyanin using explicit solvent molecular dynamics simulations. We focus on the variation in solvent cavities and the formation of tunnels in the two conformational states. By employing principal component analysis and CVAE-based deep learning, we are able to differentiate between the dynamics of the deoxy- and oxygenated states of hemocyanin. Finally, our results identify the deoxygenated open conformation, which adopts a stable, closed conformation after the oxygenation process.
Collapse
Affiliation(s)
- Khair Bux
- Third World Center for Science and Technology, H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Xiayu Shen
- UCL School of Pharmacy, London, United Kingdom
| | - Muhammad Tariq
- Third World Center for Science and Technology, H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Junqi Yin
- Oak Ridge National Laboratory, Center for Computational Sciences, Oak Ridge, TN, United States
| | - Syed Tarique Moin
- Third World Center for Science and Technology, H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Debsindhu Bhowmik
- Oak Ridge National Laboratory, Computer Sciences and Engineering Division, Oak Ridge, TN, United States
| | | |
Collapse
|
12
|
Olehnovics E, Yin J, Pérez A, De Fabritiis G, Bonomo RA, Bhowmik D, Haider S. The Role of Hydrophobic Nodes in the Dynamics of Class A β-Lactamases. Front Microbiol 2021; 12:720991. [PMID: 34621251 PMCID: PMC8490755 DOI: 10.3389/fmicb.2021.720991] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 08/09/2021] [Indexed: 11/16/2022] Open
Abstract
Class A β-lactamases are known for being able to rapidly gain broad spectrum catalytic efficiency against most β-lactamase inhibitor combinations as a result of elusively minor point mutations. The evolution in class A β-lactamases occurs through optimisation of their dynamic phenotypes at different timescales. At long-timescales, certain conformations are more catalytically permissive than others while at the short timescales, fine-grained optimisation of free energy barriers can improve efficiency in ligand processing by the active site. Free energy barriers, which define all coordinated movements, depend on the flexibility of the secondary structural elements. The most highly conserved residues in class A β-lactamases are hydrophobic nodes that stabilize the core. To assess how the stable hydrophobic core is linked to the structural dynamics of the active site, we carried out adaptively sampled molecular dynamics (MD) simulations in four representative class A β-lactamases (KPC-2, SME-1, TEM-1, and SHV-1). Using Markov State Models (MSM) and unsupervised deep learning, we show that the dynamics of the hydrophobic nodes is used as a metastable relay of kinetic information within the core and is coupled with the catalytically permissive conformation of the active site environment. Our results collectively demonstrate that the class A enzymes described here, share several important dynamic similarities and the hydrophobic nodes comprise of an informative set of dynamic variables in representative class A β-lactamases.
Collapse
Affiliation(s)
- Edgar Olehnovics
- Pharmaceutical and Biological Chemistry, University College London School of Pharmacy, London, United Kingdom
| | - Junqi Yin
- Oak Ridge National Laboratory, National Center for Computational Sciences, Oak Ridge, TN, United States
| | - Adrià Pérez
- Computational Science Laboratory, Barcelona Biomedical Research Park, Universitat Pompeu Fabra, Barcelona, Spain
| | - Gianni De Fabritiis
- Computational Science Laboratory, Barcelona Biomedical Research Park, Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Robert A. Bonomo
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, United States
- Department of Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, United States
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, United States
- Department of Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH, United States
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH, United States
- Veterans Affairs Northeast Ohio Healthcare System, Research Service, Cleveland, OH, United States
| | - Debsindhu Bhowmik
- Computer Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Shozeb Haider
- Pharmaceutical and Biological Chemistry, University College London School of Pharmacy, London, United Kingdom
| |
Collapse
|
13
|
Casalino L, Dommer AC, Gaieb Z, Barros EP, Sztain T, Ahn SH, Trifan A, Brace A, Bogetti AT, Clyde A, Ma H, Lee H, Turilli M, Khalid S, Chong LT, Simmerling C, Hardy DJ, Maia JD, Phillips JC, Kurth T, Stern AC, Huang L, McCalpin JD, Tatineni M, Gibbs T, Stone JE, Jha S, Ramanathan A, Amaro RE. AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics. THE INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS 2021; 35:432-451. [PMID: 38603008 PMCID: PMC8064023 DOI: 10.1177/10943420211006452] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
We develop a generalizable AI-driven workflow that leverages heterogeneous HPC resources to explore the time-dependent dynamics of molecular systems. We use this workflow to investigate the mechanisms of infectivity of the SARS-CoV-2 spike protein, the main viral infection machinery. Our workflow enables more efficient investigation of spike dynamics in a variety of complex environments, including within a complete SARS-CoV-2 viral envelope simulation, which contains 305 million atoms and shows strong scaling on ORNL Summit using NAMD. We present several novel scientific discoveries, including the elucidation of the spike's full glycan shield, the role of spike glycans in modulating the infectivity of the virus, and the characterization of the flexible interactions between the spike and the human ACE2 receptor. We also demonstrate how AI can accelerate conformational sampling across different systems and pave the way for the future application of such methods to additional studies in SARS-CoV-2 and other molecular systems.
Collapse
Affiliation(s)
- Lorenzo Casalino
- University of California San Diego, La Jolla, CA, USA
- Authors with symbol indicate equal contribution
| | - Abigail C Dommer
- University of California San Diego, La Jolla, CA, USA
- Authors with symbol indicate equal contribution
| | - Zied Gaieb
- University of California San Diego, La Jolla, CA, USA
- Authors with symbol indicate equal contribution
| | | | - Terra Sztain
- University of California San Diego, La Jolla, CA, USA
| | - Surl-Hee Ahn
- University of California San Diego, La Jolla, CA, USA
| | - Anda Trifan
- Argonne National Lab, Lemont, IL, USA
- University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | | | - Austin Clyde
- Argonne National Lab, Lemont, IL, USA
- University of Chicago, Chicago, IL, USA
| | - Heng Ma
- Argonne National Lab, Lemont, IL, USA
| | | | | | | | | | | | - David J Hardy
- University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Julio Dc Maia
- University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | | | | | - Lei Huang
- Texas Advanced Computing Center, Austin, TX, USA
| | | | | | - Tom Gibbs
- NVIDIA Corporation, Santa Clara, CA, USA
| | - John E Stone
- University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Shantenu Jha
- Rutgers University, Piscataway, NJ, USA
- Brookhaven National Lab, Upton, NY, USA
| | | | | |
Collapse
|
14
|
Longitudinal clinical, cognitive, and neuroanatomical changes over 5 years in GBA-positive Parkinson's disease patients. J Neurol 2021; 269:1485-1500. [PMID: 34297177 DOI: 10.1007/s00415-021-10713-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/23/2021] [Accepted: 07/11/2021] [Indexed: 10/20/2022]
Abstract
OBJECTIVE To study the longitudinal disease course of Parkinson's disease (PD) patients with glucocerebrosidase (GBA) mutation (GBA-positive) compared to PD non-carriers (GBA-negative) along a 5-year follow-up, evaluating changes in clinical and cognitive outcomes, cortical thickness, and gray-matter (GM) volumes. METHODS Ten GBA-positive and 20 GBA-negative PD patients underwent clinical, neuropsychological, and MRI assessments (cortical thickness and subcortical, hippocampal, and amygdala volumes) at study entry and once a year for 5 years. At baseline and at the last visit, each group of patients was compared with 22 age-matched healthy controls. Clinical, cognitive, and MRI features were compared between groups at baseline and over time. RESULTS At baseline, GBA-positive and GBA-negative PD patients had similar clinical and cognitive profiles. Compared to GBA-negative and controls, GBA-positive patients showed cortical thinning of left temporal, parietal, and occipital gyri. Over time, compared to GBA-negative, GBA-positive PD patients progressed significantly in motor and cognitive symptoms, and showed a greater pattern of cortical thinning of posterior regions, and frontal and orbito-frontal cortices. After 5 years, compared to controls, GBA-negative PD patients showed a pattern of cortical thinning similar to that showed by GBA-positive cases at baseline. The two groups of patients showed similar patterns of subcortical, hippocampal, and amygdala volume loss over time. CONCLUSIONS Compared to GBA-negative PD, GBA-positive patients experienced a more rapid motor and cognitive decline together with a greater, earlier and faster cortical thinning. Cortical thickness measures may be a useful tool for monitoring and predicting PD progression in accordance with the genetic background.
Collapse
|
15
|
Cho E, Rosa M, Anjum R, Mehmood S, Soban M, Mujtaba M, Bux K, Moin ST, Tanweer M, Dantu S, Pandini A, Yin J, Ma H, Ramanathan A, Islam B, Mey ASJ, Bhowmik D, Haider S. Dynamic Profiling of β-Coronavirus 3CL M pro Protease Ligand-Binding Sites. J Chem Inf Model 2021; 61:3058-3073. [PMID: 34124899 PMCID: PMC8230960 DOI: 10.1021/acs.jcim.1c00449] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Indexed: 01/11/2023]
Abstract
β-coronavirus (CoVs) alone has been responsible for three major global outbreaks in the 21st century. The current crisis has led to an urgent requirement to develop therapeutics. Even though a number of vaccines are available, alternative strategies targeting essential viral components are required as a backup against the emergence of lethal viral variants. One such target is the main protease (Mpro) that plays an indispensable role in viral replication. The availability of over 270 Mpro X-ray structures in complex with inhibitors provides unique insights into ligand-protein interactions. Herein, we provide a comprehensive comparison of all nonredundant ligand-binding sites available for SARS-CoV2, SARS-CoV, and MERS-CoV Mpro. Extensive adaptive sampling has been used to investigate structural conservation of ligand-binding sites using Markov state models (MSMs) and compare conformational dynamics employing convolutional variational auto-encoder-based deep learning. Our results indicate that not all ligand-binding sites are dynamically conserved despite high sequence and structural conservation across β-CoV homologs. This highlights the complexity in targeting all three Mpro enzymes with a single pan inhibitor.
Collapse
Affiliation(s)
- Eunice Cho
- UCL
School of Pharmacy, London WC1N 1AX, U.K.
| | | | - Ruhi Anjum
- Department
of Biochemistry, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002, India
| | - Saman Mehmood
- Department
of Zoology, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002, India
| | - Mariya Soban
- Department
of Biochemistry, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002, India
| | - Moniza Mujtaba
- Herricks
High School, New Hyde
Park, New York 11040 United States
| | - Khair Bux
- Third
World Center for Science and Technology, H.E.J. Research Institute
of Chemistry, International Centre of Chemical and Biological Sciences, University of Karachi, Karachi 75270 Pakistan
| | - Syed T. Moin
- Third
World Center for Science and Technology, H.E.J. Research Institute
of Chemistry, International Centre of Chemical and Biological Sciences, University of Karachi, Karachi 75270 Pakistan
| | | | - Sarath Dantu
- Department
of Computer Science, Brunel University, Uxbridge UB8 3PH, U.K.
| | - Alessandro Pandini
- Department
of Computer Science, Brunel University, Uxbridge UB8 3PH, U.K.
| | - Junqi Yin
- Center
for Computational Sciences, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Heng Ma
- Data
Science and Learning Division, Argonne National
Laboratory, Lemont, Illinois 60439, United States
| | - Arvind Ramanathan
- Data
Science and Learning Division, Argonne National
Laboratory, Lemont, Illinois 60439, United States
- Consortium
for Advanced Science and Engineering, University
of Chicago, Chicago, Illinois 60637, United
States
| | - Barira Islam
- Department
of Bioscience, University of Huddersfield, Huddersfield HD1 3DH, U.K.
| | - Antonia S. J.
S. Mey
- EaStCHEM
School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, U.K.
| | - Debsindhu Bhowmik
- Computer
Sciences and Engineering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37830, United States
| | | |
Collapse
|
16
|
Sandin SI, Gravano DM, Randolph CJ, Sharma M, de Alba E. Engineering of Saposin C Protein Chimeras for Enhanced Cytotoxicity and Optimized Liposome Binding Capability. Pharmaceutics 2021; 13:pharmaceutics13040583. [PMID: 33921905 PMCID: PMC8072984 DOI: 10.3390/pharmaceutics13040583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/11/2021] [Accepted: 04/14/2021] [Indexed: 02/04/2023] Open
Abstract
Saposin C (sapC) is a lysosomal, peripheral-membrane protein displaying liposome fusogenic capabilities. Proteoliposomes of sapC and phosphatidylserine have been shown to be toxic for cancer cells and are currently on clinical trial to treat glioblastoma. As proof-of-concept, we show two strategies to enhance the applications of sapC proteoliposomes: (1) Engineering chimeras composed of sapC to modulate proteoliposome function; (2) Engineering sapC to modify its lipid binding capabilities. In the chimera design, sapC is linked to a cell death-inducing peptide: the BH3 domain of the Bcl-2 protein PUMA. We show by solution NMR and dynamic light scattering that the chimera is functional at the molecular level by fusing liposomes and by interacting with prosurvival Bcl-xL, which is PUMA’s known mechanism to induce cell death. Furthermore, sapC-PUMA proteoliposomes enhance cytotoxicity in glioblastoma cells compared to sapC. Finally, the sapC domain of the chimera has been engineered to optimize liposome binding at pH close to physiological values as protein–lipid interactions are favored at acidic pH in the native protein. Altogether, our results indicate that the properties of sapC proteoliposomes can be modified by engineering the protein surface and by the addition of small peptides as fusion constructs.
Collapse
Affiliation(s)
- Suzanne I. Sandin
- Department of Bioengineering, University of California, Merced, CA 95343, USA; (S.I.S.); (C.J.R.); (M.S.)
- Chemistry and Chemical Biology Ph.D. Program, University of California, Merced, CA 95343, USA
| | - David M. Gravano
- Stem Cell Instrumentation Foundry, University of California, Merced, CA 95343, USA;
| | - Christopher J. Randolph
- Department of Bioengineering, University of California, Merced, CA 95343, USA; (S.I.S.); (C.J.R.); (M.S.)
| | - Meenakshi Sharma
- Department of Bioengineering, University of California, Merced, CA 95343, USA; (S.I.S.); (C.J.R.); (M.S.)
| | - Eva de Alba
- Department of Bioengineering, University of California, Merced, CA 95343, USA; (S.I.S.); (C.J.R.); (M.S.)
- Correspondence:
| |
Collapse
|
17
|
Blanchard AE, Stanley C, Bhowmik D. Using GANs with adaptive training data to search for new molecules. J Cheminform 2021; 13:14. [PMID: 33622401 PMCID: PMC7901067 DOI: 10.1186/s13321-021-00494-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/09/2021] [Indexed: 11/10/2022] Open
Abstract
The process of drug discovery involves a search over the space of all possible chemical compounds. Generative Adversarial Networks (GANs) provide a valuable tool towards exploring chemical space and optimizing known compounds for a desired functionality. Standard approaches to training GANs, however, can result in mode collapse, in which the generator primarily produces samples closely related to a small subset of the training data. In contrast, the search for novel compounds necessitates exploration beyond the original data. Here, we present an approach to training GANs that promotes incremental exploration and limits the impacts of mode collapse using concepts from Genetic Algorithms. In our approach, valid samples from the generator are used to replace samples from the training data. We consider both random and guided selection along with recombination during replacement. By tracking the number of novel compounds produced during training, we show that updates to the training data drastically outperform the traditional approach, increasing potential applications for GANs in drug discovery.
Collapse
Affiliation(s)
- Andrew E Blanchard
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Christopher Stanley
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Debsindhu Bhowmik
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.
| |
Collapse
|
18
|
Kopytova AE, Rychkov GN, Nikolaev MA, Baydakova GV, Cheblokov AA, Senkevich KA, Bogdanova DA, Bolshakova OI, Miliukhina IV, Bezrukikh VA, Salogub GN, Sarantseva SV, Usenko TC, Zakharova EY, Emelyanov AK, Pchelina SN. Ambroxol increases glucocerebrosidase (GCase) activity and restores GCase translocation in primary patient-derived macrophages in Gaucher disease and Parkinsonism. Parkinsonism Relat Disord 2021; 84:112-121. [PMID: 33609962 DOI: 10.1016/j.parkreldis.2021.02.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 01/11/2021] [Accepted: 02/01/2021] [Indexed: 12/24/2022]
Abstract
Mutations in the glucocerebrosidase gene (GBA) encoding the lysosomal enzyme glucocerebrosidase (GCase) cause Gaucher disease (GD) and are the most commonly known genetic risk factor for Parkinson disease (PD). Ambroxol is one of the most effective pharmacological chaperones of GCase. Fourteen GD patients, six PD patients with mutations in the GBA gene (GBA-PD), and thirty controls were enrolled. GCase activity and hexosylsphingosine (HexSph) concentration were measured in dried blood and macrophage spots using liquid chromatography coupled with tandem mass spectrometry. The effect of ambroxol on GCase translocation to lysosomes was assessed using confocal microscopy. The results showed that ambroxol treatment significantly increased GCase activity in cultured macrophages derived from patient blood monocytic cell (PBMC) of GD (by 3.3-fold) and GBA-PD patients (by 3.5-fold) compared to untreated cells (p < 0.0001 and p < 0.0001, respectively) four days after cultivation. Ambroxol treatment significantly reduced HexSph concentration in GD (by 2.1-fold) and GBA-PD patients (by 1.6-fold) (p < 0.0001 and p < 0.0001, respectively). GD macrophage treatment resulted in increased GCase level and increased enzyme colocalization with the lysosomal marker LAMP2. The possible binding modes of ambroxol to mutant GCase carrying N370S amino acid substitution at pH 4.7 were examined using molecular docking and molecular dynamics simulations. The ambroxol position characterized by minimal binding free energy was observed in close vicinity to the residue, at position 370. Taken together, these data showed that PBMC-derived macrophages could be used for assessing ambroxol therapy response for GD patients and also for GBA-PD patients.
Collapse
Affiliation(s)
- A E Kopytova
- Petersburg Nuclear Physics Institute Named By B.P. Konstantinov of National Research Center «Kurchatov Institute», Gatchina, Russia.
| | - G N Rychkov
- Petersburg Nuclear Physics Institute Named By B.P. Konstantinov of National Research Center «Kurchatov Institute», Gatchina, Russia; Peter the Great St.Petersburg Polytechnic University, Saint-Petersburg, Russia; Kurchatov Genome Center - PNPI, Gatchina, Russia
| | - M A Nikolaev
- Petersburg Nuclear Physics Institute Named By B.P. Konstantinov of National Research Center «Kurchatov Institute», Gatchina, Russia; First Pavlov State Medical University of St. Petersburg, Saint-Petersburg, Russia
| | - G V Baydakova
- Research Center for Medical Genetics, Moscow, Russia
| | - A A Cheblokov
- Petersburg Nuclear Physics Institute Named By B.P. Konstantinov of National Research Center «Kurchatov Institute», Gatchina, Russia
| | - K A Senkevich
- Petersburg Nuclear Physics Institute Named By B.P. Konstantinov of National Research Center «Kurchatov Institute», Gatchina, Russia; First Pavlov State Medical University of St. Petersburg, Saint-Petersburg, Russia
| | - D A Bogdanova
- Petersburg Nuclear Physics Institute Named By B.P. Konstantinov of National Research Center «Kurchatov Institute», Gatchina, Russia
| | - O I Bolshakova
- Petersburg Nuclear Physics Institute Named By B.P. Konstantinov of National Research Center «Kurchatov Institute», Gatchina, Russia
| | - I V Miliukhina
- Petersburg Nuclear Physics Institute Named By B.P. Konstantinov of National Research Center «Kurchatov Institute», Gatchina, Russia; Institute of Experimental Medicine, Saint-Petersburg, Russia; First Pavlov State Medical University of St. Petersburg, Saint-Petersburg, Russia
| | - V A Bezrukikh
- Almazov National Medical Research Centre, Saint-Petersburg, Russia
| | - G N Salogub
- Almazov National Medical Research Centre, Saint-Petersburg, Russia
| | - S V Sarantseva
- Petersburg Nuclear Physics Institute Named By B.P. Konstantinov of National Research Center «Kurchatov Institute», Gatchina, Russia
| | - T C Usenko
- Petersburg Nuclear Physics Institute Named By B.P. Konstantinov of National Research Center «Kurchatov Institute», Gatchina, Russia; First Pavlov State Medical University of St. Petersburg, Saint-Petersburg, Russia
| | - E Y Zakharova
- Research Center for Medical Genetics, Moscow, Russia
| | - A K Emelyanov
- Petersburg Nuclear Physics Institute Named By B.P. Konstantinov of National Research Center «Kurchatov Institute», Gatchina, Russia; Institute of Experimental Medicine, Saint-Petersburg, Russia; First Pavlov State Medical University of St. Petersburg, Saint-Petersburg, Russia
| | - S N Pchelina
- Petersburg Nuclear Physics Institute Named By B.P. Konstantinov of National Research Center «Kurchatov Institute», Gatchina, Russia; Institute of Experimental Medicine, Saint-Petersburg, Russia; First Pavlov State Medical University of St. Petersburg, Saint-Petersburg, Russia
| |
Collapse
|
19
|
Grabowski GA, Antommaria AHM, Kolodny EH, Mistry PK. Gaucher disease: Basic and translational science needs for more complete therapy and management. Mol Genet Metab 2021; 132:59-75. [PMID: 33419694 PMCID: PMC8809485 DOI: 10.1016/j.ymgme.2020.12.291] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/15/2020] [Accepted: 12/18/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Gregory A Grabowski
- Department of Pediatrics, University of Cincinnati College of Medicine, United States of America; Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, United States of America; Division of Human Genetics, Cincinnati Children's Research Foundation, Cincinnati, OH, United States of America.
| | - Armand H M Antommaria
- Department of Pediatrics, University of Cincinnati College of Medicine, United States of America; Lee Ault Carter Chair of Pediatric Ethics, Cincinnati Children's Research Foundation, Cincinnati, OH, United States of America.
| | - Edwin H Kolodny
- Department of Neurology, New York University Grossman School of Medicine, New York, NY, United States of America.
| | - Pramod K Mistry
- Departments of Medicine and Pediatrics, Yale School of Medicine, New Haven, CT, United States of America.
| |
Collapse
|
20
|
Ramanathan A, Ma H, Parvatikar A, Chennubhotla SC. Artificial intelligence techniques for integrative structural biology of intrinsically disordered proteins. Curr Opin Struct Biol 2021; 66:216-224. [PMID: 33421906 DOI: 10.1016/j.sbi.2020.12.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/01/2020] [Accepted: 12/03/2020] [Indexed: 12/16/2022]
Abstract
We outline recent developments in artificial intelligence (AI) and machine learning (ML) techniques for integrative structural biology of intrinsically disordered proteins (IDP) ensembles. IDPs challenge the traditional protein structure-function paradigm by adapting their conformations in response to specific binding partners leading them to mediate diverse, and often complex cellular functions such as biological signaling, self-organization and compartmentalization. Obtaining mechanistic insights into their function can therefore be challenging for traditional structural determination techniques. Often, scientists have to rely on piecemeal evidence drawn from diverse experimental techniques to characterize their functional mechanisms. Multiscale simulations can help bridge critical knowledge gaps about IDP structure-function relationships-however, these techniques also face challenges in resolving emergent phenomena within IDP conformational ensembles. We posit that scalable statistical inference techniques can effectively integrate information gleaned from multiple experimental techniques as well as from simulations, thus providing access to atomistic details of these emergent phenomena.
Collapse
Affiliation(s)
- Arvind Ramanathan
- Data Science & Learning Division, Argonne National Laboratory, Lemont, IL 60439, United States; Consortium for Advanced Science and Engineering (CASE), University of Chicago, Hyde Park, IL, United States.
| | - Heng Ma
- Data Science & Learning Division, Argonne National Laboratory, Lemont, IL 60439, United States
| | - Akash Parvatikar
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - S Chakra Chennubhotla
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, United States
| |
Collapse
|
21
|
Acharya A, Agarwal R, Baker M, Baudry J, Bhowmik D, Boehm S, Byler KG, Chen S, Coates L, Cooper C, Demerdash O, Daidone I, Eblen J, Ellingson S, Forli S, Glaser J, Gumbart JC, Gunnels J, Hernandez O, Irle S, Kneller D, Kovalevsky A, Larkin J, Lawrence T, LeGrand S, Liu SH, Mitchell J, Park G, Parks J, Pavlova A, Petridis L, Poole D, Pouchard L, Ramanathan A, Rogers D, Santos-Martins D, Scheinberg A, Sedova A, Shen Y, Smith J, Smith M, Soto C, Tsaris A, Thavappiragasam M, Tillack A, Vermaas J, Vuong V, Yin J, Yoo S, Zahran M, Zanetti-Polzi L. Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19. J Chem Inf Model 2020; 60:5832-5852. [PMID: 33326239 PMCID: PMC7754786 DOI: 10.1021/acs.jcim.0c01010] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Indexed: 01/18/2023]
Abstract
We present a supercomputer-driven pipeline for in silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. Ensemble docking makes use of MD results by docking compound databases into representative protein binding-site conformations, thus taking into account the dynamic properties of the binding sites. We also describe preliminary results obtained for 24 systems involving eight proteins of the proteome of SARS-CoV-2. The MD involves temperature replica exchange enhanced sampling, making use of massively parallel supercomputing to quickly sample the configurational space of protein drug targets. Using the Summit supercomputer at the Oak Ridge National Laboratory, more than 1 ms of enhanced sampling MD can be generated per day. We have ensemble docked repurposing databases to 10 configurations of each of the 24 SARS-CoV-2 systems using AutoDock Vina. Comparison to experiment demonstrates remarkably high hit rates for the top scoring tranches of compounds identified by our ensemble approach. We also demonstrate that, using Autodock-GPU on Summit, it is possible to perform exhaustive docking of one billion compounds in under 24 h. Finally, we discuss preliminary results and planned improvements to the pipeline, including the use of quantum mechanical (QM), machine learning, and artificial intelligence (AI) methods to cluster MD trajectories and rescore docking poses.
Collapse
Affiliation(s)
- A. Acharya
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - R. Agarwal
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830, USA
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996, USA
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - M. Baker
- Computer Science and Mathematics Division, Oak Ridge National Lab, Oak Ridge, TN 37830, USA
| | - J. Baudry
- The University of Alabama in Huntsville, Department of Biological Sciences. 301 Sparkman Drive, Huntsville, AL 35899, USA
| | - D. Bhowmik
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - S. Boehm
- Computer Science and Mathematics Division, Oak Ridge National Lab, Oak Ridge, TN 37830, USA
| | - K. G. Byler
- The University of Alabama in Huntsville, Department of Biological Sciences. 301 Sparkman Drive, Huntsville, AL 35899, USA
| | - S.Y. Chen
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - L. Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - C.J. Cooper
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830, USA
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - O. Demerdash
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37830, USA
| | - I. Daidone
- Department of Physical and Chemical Sciences, University of L’Aquila, I-67010 L’Aquila, Italy
| | - J.D. Eblen
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830, USA
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996, USA
| | - S. Ellingson
- University of Kentucky, Division of Biomedical Informatics, College of Medicine, UK Medical Center MN 150, Lexington KY, 40536, USA
| | - S. Forli
- Scripps Research, La Jolla, CA, 92037, USA
| | - J. Glaser
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - J. C. Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - J. Gunnels
- HPC Engineering, Amazon Web Services, Seattle, WA 98121, USA
| | - O. Hernandez
- Computer Science and Mathematics Division, Oak Ridge National Lab, Oak Ridge, TN 37830, USA
| | - S. Irle
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN 37996, USA
| | - D.W. Kneller
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - A. Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - J. Larkin
- NVIDIA Corporation, Santa Clara, CA 95051, USA
| | - T.J. Lawrence
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37830, USA
| | - S. LeGrand
- NVIDIA Corporation, Santa Clara, CA 95051, USA
| | - S.-H. Liu
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830, USA
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996, USA
| | - J.C. Mitchell
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37830, USA
| | - G. Park
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - J.M. Parks
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830, USA
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996, USA
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - A. Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - L. Petridis
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830, USA
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996, USA
| | - D. Poole
- NVIDIA Corporation, Santa Clara, CA 95051, USA
| | - L. Pouchard
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - A. Ramanathan
- Data Science and Learning Division, Argonne National Lab, Lemont, IL 60439, USA
| | - D. Rogers
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | | | | | - A. Sedova
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37830, USA
| | - Y. Shen
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830, USA
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996, USA
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - J.C. Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830, USA
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996, USA
| | - M.D. Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830, USA
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996, USA
| | - C. Soto
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - A. Tsaris
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | | | | | - J.V. Vermaas
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - V.Q. Vuong
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN 37996, USA
| | - J. Yin
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - S. Yoo
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - M. Zahran
- Department of Biological Sciences, New York City College of Technology, The City University of New York (CUNY), Brooklyn, NY 11201, USA
| | | |
Collapse
|
22
|
The interplay between Glucocerebrosidase, α-synuclein and lipids in human models of Parkinson's disease. Biophys Chem 2020; 273:106534. [PMID: 33832803 DOI: 10.1016/j.bpc.2020.106534] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/18/2020] [Accepted: 12/18/2020] [Indexed: 12/25/2022]
Abstract
Mutations in the gene GBA, encoding glucocerebrosidase (GCase), are the highest genetic risk factor for Parkinson's disease (PD). GCase is a lysosomal glycoprotein responsible for the hydrolysis of glucosylceramide into glucose and ceramide. Mutations in GBA cause a decrease in GCase activity, stability and protein levels which in turn lead to the accumulation of GCase lipid substrates as well as α-synuclein (αS) in vitro and in vivo. αS is the main constituent of Lewy bodies found in the brain of PD patients and an increase in its levels was found to be associated with a decrease in GCase activity/protein levels in vitro and in vivo. In this review, we describe the reported biophysical and biochemical changes that GBA mutations can induce in GCase activity and stability as well as the current overview of the levels of GCase protein/activity, αS and lipids measured in patient-derived samples including post-mortem brains, stem cell-derived neurons, cerebrospinal fluid, blood and fibroblasts as well as in SH-SY5Y cells. In particular, we report how the levels of αS and lipids are affected by/correlated to significant changes in GCase activity/protein levels and which cellular pathways are activated or disrupted by these changes in each model. Finally, we review the current strategies used to revert the changes in the levels of GCase activity/protein, αS and lipids in the context of PD.
Collapse
|
23
|
Wan S, Bhati AP, Zasada SJ, Coveney PV. Rapid, accurate, precise and reproducible ligand-protein binding free energy prediction. Interface Focus 2020; 10:20200007. [PMID: 33178418 PMCID: PMC7653346 DOI: 10.1098/rsfs.2020.0007] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2020] [Indexed: 02/06/2023] Open
Abstract
A central quantity of interest in molecular biology and medicine is the free energy of binding of a molecule to a target biomacromolecule. Until recently, the accurate prediction of binding affinity had been widely regarded as out of reach of theoretical methods owing to the lack of reproducibility of the available methods, not to mention their complexity, computational cost and time-consuming procedures. The lack of reproducibility stems primarily from the chaotic nature of classical molecular dynamics (MD) and the associated extreme sensitivity of trajectories to their initial conditions. Here, we review computational approaches for both relative and absolute binding free energy calculations, and illustrate their application to a diverse set of ligands bound to a range of proteins with immediate relevance in a number of medical domains. We focus on ensemble-based methods which are essential in order to compute statistically robust results, including two we have recently developed, namely thermodynamic integration with enhanced sampling and enhanced sampling of MD with an approximation of continuum solvent. Together, these form a set of rapid, accurate, precise and reproducible free energy methods. They can be used in real-world problems such as hit-to-lead and lead optimization stages in drug discovery, and in personalized medicine. These applications show that individual binding affinities equipped with uncertainty quantification may be computed in a few hours on a massive scale given access to suitable high-end computing resources and workflow automation. A high level of accuracy can be achieved using these approaches.
Collapse
Affiliation(s)
- Shunzhou Wan
- Centre for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, UK
| | - Agastya P. Bhati
- Centre for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, UK
| | - Stefan J. Zasada
- Centre for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, UK
| | - Peter V. Coveney
- Centre for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, UK
- Computational Science Laboratory, Institute for Informatics, Faculty of Science, University of Amsterdam, 1098XH Amsterdam, The Netherlands
| |
Collapse
|
24
|
Casalino L, Dommer A, Gaieb Z, Barros EP, Sztain T, Ahn SH, Trifan A, Brace A, Bogetti A, Ma H, Lee H, Turilli M, Khalid S, Chong L, Simmerling C, Hardy DJ, Maia JDC, Phillips JC, Kurth T, Stern A, Huang L, McCalpin J, Tatineni M, Gibbs T, Stone JE, Jha S, Ramanathan A, Amaro RE. AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.11.19.390187. [PMID: 33236007 PMCID: PMC7685317 DOI: 10.1101/2020.11.19.390187] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2023]
Abstract
We develop a generalizable AI-driven workflow that leverages heterogeneous HPC resources to explore the time-dependent dynamics of molecular systems. We use this workflow to investigate the mechanisms of infectivity of the SARS-CoV-2 spike protein, the main viral infection machinery. Our workflow enables more efficient investigation of spike dynamics in a variety of complex environments, including within a complete SARS-CoV-2 viral envelope simulation, which contains 305 million atoms and shows strong scaling on ORNL Summit using NAMD. We present several novel scientific discoveries, including the elucidation of the spike's full glycan shield, the role of spike glycans in modulating the infectivity of the virus, and the characterization of the flexible interactions between the spike and the human ACE2 receptor. We also demonstrate how AI can accelerate conformational sampling across different systems and pave the way for the future application of such methods to additional studies in SARS-CoV-2 and other molecular systems.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Anda Trifan
- Argonne National Lab
- University of Illinois at Urbana-Champaign
| | | | | | | | - Hyungro Lee
- Rutgers University & Brookhaven National Lab
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Dupuis JH, Wang S, Song C, Yada RY. The role of disulfide bonds in a Solanum tuberosum saposin-like protein investigated using molecular dynamics. PLoS One 2020; 15:e0237884. [PMID: 32841243 PMCID: PMC7447066 DOI: 10.1371/journal.pone.0237884] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/04/2020] [Indexed: 01/31/2023] Open
Abstract
The Solanum tuberosum plant specific insert (StPSI) has a defensive role in potato plants, with the requirements of acidic pH and anionic lipids. The StPSI contains a set of three highly conserved disulfide bonds that bridge the protein’s helical domains. Removal of these bonds leads to enhanced membrane interactions. This work examined the effects of their sequential removal, both individually and in combination, using all-atom molecular dynamics to elucidate the role of disulfide linkages in maintaining overall protein tertiary structure. The tertiary structure was found to remain stable at both acidic (active) and neutral (inactive) pH despite the removal of disulfide linkages. The findings include how the dimer structure is stabilized and the impact on secondary structure on a residue-basis as a function of disulfide bond removal. The StPSI possesses an extensive network of inter-monomer hydrophobic interactions and intra-monomer hydrogen bonds, which is likely the key to the stability of the StPSI by stabilizing local secondary structure and the tertiary saposin-fold, leading to a robust association between monomers, regardless of the disulfide bond state. Removal of disulfide bonds did not significantly impact secondary structure, nor lead to quaternary structural changes. Instead, disulfide bond removal induces regions of amino acids with relatively higher or lower variation in secondary structure, relative to when all the disulfide bonds are intact. Although disulfide bonds are not required to preserve overall secondary structure, they may have an important role in maintaining a less plastic structure within plant cells in order to regulate membrane affinity or targeting.
Collapse
Affiliation(s)
- John H. Dupuis
- Food, Nutrition, and Health Program, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada
| | - Shenlin Wang
- College of Chemistry and Molecular Engineering and Beijing NMR Center, Peking University, Beijing, People's Republic of China
| | - Chen Song
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, People’s Republic of China
| | - Rickey Y. Yada
- Food, Nutrition, and Health Program, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
| |
Collapse
|
26
|
Acharya A, Agarwal R, Baker M, Baudry J, Bhowmik D, Boehm S, Byler KG, Coates L, Chen SY, Cooper CJ, Demerdash O, Daidone I, Eblen JD, Ellingson S, Forli S, Glaser J, Gumbart JC, Gunnels J, Hernandez O, Irle S, Larkin J, Lawrence TJ, LeGrand S, Liu SH, Mitchell JC, Park G, Parks JM, Pavlova A, Petridis L, Poole D, Pouchard L, Ramanathan A, Rogers D, Santos-Martins D, Scheinberg A, Sedova A, Shen S, Smith JC, Smith MD, Soto C, Tsaris A, Thavappiragasam M, Tillack AF, Vermaas JV, Vuong VQ, Yin J, Yoo S, Zahran M, Zanetti-Polzi L. Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19. CHEMRXIV : THE PREPRINT SERVER FOR CHEMISTRY 2020:12725465. [PMID: 33200117 PMCID: PMC7668744 DOI: 10.26434/chemrxiv.12725465] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 07/29/2020] [Indexed: 01/18/2023]
Abstract
We present a supercomputer-driven pipeline for in-silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. We also describe preliminary results obtained for 23 systems involving eight protein targets of the proteome of SARS CoV-2. THe MD performed is temperature replica-exchange enhanced sampling, making use of the massively parallel supercomputing on the SUMMIT supercomputer at Oak Ridge National Laboratory, with which more than 1ms of enhanced sampling MD can be generated per day. We have ensemble docked repurposing databases to ten configurations of each of the 23 SARS CoV-2 systems using AutoDock Vina. We also demonstrate that using Autodock-GPU on SUMMIT, it is possible to perform exhaustive docking of one billion compounds in under 24 hours. Finally, we discuss preliminary results and planned improvements to the pipeline, including the use of quantum mechanical (QM), machine learning, and AI methods to cluster MD trajectories and rescore docking poses.
Collapse
Affiliation(s)
- A Acharya
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332
| | - R Agarwal
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996
| | - M Baker
- Computer Science and Mathematics Division, Oak Ridge National Lab, Oak Ridge, TN 37830
| | - J Baudry
- The University of Alabama in Huntsville, Department of Biological Sciences. 301 Sparkman Drive, Huntsville, AL 35899
| | - D Bhowmik
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - S Boehm
- Computer Science and Mathematics Division, Oak Ridge National Lab, Oak Ridge, TN 37830
| | - K G Byler
- The University of Alabama in Huntsville, Department of Biological Sciences. 301 Sparkman Drive, Huntsville, AL 35899
| | - L Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - S Y Chen
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973
| | - C J Cooper
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996
| | - O Demerdash
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37830
| | - I Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila, I-67010 L'Aquila, Italy
| | - J D Eblen
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996
| | - S Ellingson
- University of Kentucky, Division of Biomedical Informatics, College of Medicine, UK Medical Center MN 150, Lexington KY, 40536
| | - S Forli
- Scripps Research, La Jolla, CA, 92037
| | - J Glaser
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830
| | - J C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332
| | - J Gunnels
- HPC Engineering, Amazon Web Services, Seattle, WA 98121
| | - O Hernandez
- Computer Science and Mathematics Division, Oak Ridge National Lab, Oak Ridge, TN 37830
| | - S Irle
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN 37996
| | - J Larkin
- NVIDIA Corporation, Santa Clara, CA 95051
| | - T J Lawrence
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37830
| | - S LeGrand
- NVIDIA Corporation, Santa Clara, CA 95051
| | - S-H Liu
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996
| | - J C Mitchell
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37830
| | - G Park
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973
| | - J M Parks
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996
| | - A Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332
| | - L Petridis
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996
| | - D Poole
- NVIDIA Corporation, Santa Clara, CA 95051
| | - L Pouchard
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973
| | - A Ramanathan
- Data Science and Learning Division, Argonne National Lab, Lemont, IL 60439
| | - D Rogers
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830
| | | | | | - A Sedova
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37830
| | - S Shen
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996
| | - J C Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996
| | - M D Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN, 37830
- The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue Knoxville, TN, 37996
| | - C Soto
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973
| | - A Tsaris
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830
| | | | | | - J V Vermaas
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830
| | - V Q Vuong
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN 37996
| | - J Yin
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37830
| | - S Yoo
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973
| | - M Zahran
- Department of Biological Sciences, New York City College of Technology, The City University of New York (CUNY), Brooklyn, NY 11201
| | | |
Collapse
|
27
|
Chen Q, Xiao Y, Shakhnovich EI, Zhang W, Mu W. Semi-rational design and molecular dynamics simulations study of the thermostability enhancement of cellobiose 2-epimerases. Int J Biol Macromol 2020; 154:1356-1365. [DOI: 10.1016/j.ijbiomac.2019.11.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/29/2019] [Accepted: 11/04/2019] [Indexed: 01/19/2023]
|
28
|
Wu Y, Hui J, Deng Q. Empirical profile Bayesian estimation for extrapolation of historical adult data to pediatric drug development. Pharm Stat 2020; 19:787-802. [PMID: 32573051 DOI: 10.1002/pst.2031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 04/10/2020] [Accepted: 05/04/2020] [Indexed: 11/07/2022]
Abstract
For pediatric drug development, the clinical effectiveness of the study medication for the adult population has already been demonstrated. Given the fact that it is usually not feasible to enroll a large number of pediatric patients, appropriately leveraging historical adult data into pediatric evaluation may be critical to success of pediatric drug development. In this manuscript, we propose a new empirical Bayesian approach, profile Bayesian estimation, to dynamically borrow adult information to the evaluation of treatment effect in pediatric patients. The new approach demonstrates an attractive balance between type I error control and power gain under the transfer-ability assumption that the pediatric treatment effect size may differ from the adult treatment effect size. The decision making boundary mimics the real-world practice in pediatric drug development. In addition, the posterior mean of the proposed empirical profile Bayesian is an unbiased estimator of the true pediatric treatment effect. We compare our approach to robust mixture prior with prior weight for informative borrowing set to 0.5 or 0.9, regular Bayesian approach, and frequentist for both type I error and power.
Collapse
Affiliation(s)
- Yaoshi Wu
- Biostatistics & Data Sciences (BDS), Boehringer-Ingelheim, Ridgefield, Connecticut, USA
| | - Jianan Hui
- Biostatistics & Data Sciences (BDS), Boehringer-Ingelheim, Ridgefield, Connecticut, USA
| | - Qiqi Deng
- Biostatistics & Data Sciences (BDS), Boehringer-Ingelheim, Ridgefield, Connecticut, USA
| |
Collapse
|
29
|
Aasly JO. Long-Term Outcomes of Genetic Parkinson's Disease. J Mov Disord 2020; 13:81-96. [PMID: 32498494 PMCID: PMC7280945 DOI: 10.14802/jmd.19080] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 03/23/2020] [Indexed: 12/12/2022] Open
Abstract
Parkinson’s disease (PD) is a progressive neurodegenerative disorder that affects 1–2% of people by the age of 70 years. Age is the most important risk factor, and most cases are sporadic without any known environmental or genetic causes. Since the late 1990s, mutations in the genes SNCA, PRKN, LRRK2, PINK1, DJ-1, VPS35, and GBA have been shown to be important risk factors for PD. In addition, common variants with small effect sizes are now recognized to modulate the risk for PD. Most studies in genetic PD have focused on finding new genes, but few have studied the long-term outcome of patients with the specific genetic PD forms. Patients with known genetic PD have now been followed for more than 20 years, and we see that they may have distinct and different prognoses. New therapeutic possibilities are emerging based on the genetic cause underlying the disease. Future medication may be based on the pathophysiology individualized to the patient’s genetic background. The challenge is to find the biological consequences of different genetic variants. In this review, the clinical patterns and long-term prognoses of the most common genetic PD variants are presented.
Collapse
Affiliation(s)
- Jan O Aasly
- Department of Neurology, St. Olav's Hospital, Trondheim, Norway.,Department of Neuroscience, Norwegian University of Science and Technology, Trondheim, Norway
| |
Collapse
|
30
|
Simple and Complex Sugars in Parkinson's Disease: a Bittersweet Taste. Mol Neurobiol 2020; 57:2934-2943. [PMID: 32430844 DOI: 10.1007/s12035-020-01931-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/01/2020] [Indexed: 12/18/2022]
Abstract
Neuronal homeostasis depends on both simple and complex sugars (the glycoconjugates), and derangement of their metabolism is liable to impair neural function and lead to neurodegeneration. Glucose levels boost glycation phenomena, a wide series of non-enzymatic reactions that give rise to various intermediates and end-products that are potentially dangerous in neurons. Glycoconjugates, including glycoproteins, glycolipids, and glycosaminoglycans, contribute to the constitution of the unique features of neuron membranes and extracellular matrix in the nervous system. Glycosylation defects are indeed frequently associated with nervous system disturbances and neurodegeneration. Parkinson's disease (PD) is a neurodegenerative disorder characterized by motor and non-motor symptoms associated with the loss of dopaminergic neurons in the pars compacta of the substantia nigra. Neurons present intracytoplasmic inclusions of α-synuclein aggregates involved in the disease pathogenesis together with the impairment of the autophagy-lysosome function, oxidative stress, and defective traffic and turnover of membrane components. In the present review, we selected relevant recent contributions concerning the direct involvement of glycation and glycosylation in α-synuclein stability, impaired autophagy and lysosomal function in PD, focusing on potential models of PD pathogenesis provided by genetic variants of glycosphingolipid processing enzymes, especially glucocerebrosidase (GBA). Moreover, we collected data aimed at defining the glycomic profile of PD patients as a tool to help in diagnosis and patient subtyping, as well as those pointing to sugar-related compounds with potential therapeutic applications in PD.
Collapse
|
31
|
Molecular models should not be published without the corresponding atomic coordinates. Proc Natl Acad Sci U S A 2020; 116:11099-11100. [PMID: 31164476 DOI: 10.1073/pnas.1904409116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
32
|
Shiref H, Bergman S, Clivio S, Sahai MA. The fine art of preparing membrane transport proteins for biomolecular simulations: Concepts and practical considerations. Methods 2020; 185:3-14. [PMID: 32081744 PMCID: PMC10062712 DOI: 10.1016/j.ymeth.2020.02.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 02/14/2020] [Accepted: 02/14/2020] [Indexed: 10/25/2022] Open
Abstract
Molecular dynamics (MD) simulations have developed into an invaluable tool in bimolecular research, due to the capability of the method in capturing molecular events and structural transitions that describe the function as well as the physiochemical properties of biomolecular systems. Due to the progressive development of more efficient algorithms, expansion of the available computational resources, as well as the emergence of more advanced methodologies, the scope of computational studies has increased vastly over time. We now have access to a multitude of online databases, software packages, larger molecular systems and novel ligands due to the phenomenon of emerging novel psychoactive substances (NPS). With so many advances in the field, it is understandable that novices will no doubt find it challenging setting up a protein-ligand system even before they run their first MD simulation. These initial steps, such as homology modelling, ligand docking, parameterization, protein preparation and membrane setup have become a fundamental part of the drug discovery pipeline, and many areas of biomolecular sciences benefit from the applications provided by these technologies. However, there still remains no standard on their usage. Therefore, our aim within this review is to provide a clear overview of a variety of concepts and methodologies to consider, providing a workflow for a case study of a membrane transport protein, the full-length human dopamine transporter (hDAT) in complex with different stimulants, where MD simulations have recently been applied successfully.
Collapse
Affiliation(s)
- Hana Shiref
- Department of Life Sciences, University of Roehampton, London SW15 4JD, UK
| | - Shana Bergman
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC), New York, NY 10065, USA
| | | | - Michelle A Sahai
- Department of Life Sciences, University of Roehampton, London SW15 4JD, UK.
| |
Collapse
|
33
|
Toffoli M, Smith L, Schapira AHV. The biochemical basis of interactions between Glucocerebrosidase and alpha-synuclein in GBA1 mutation carriers. J Neurochem 2020; 154:11-24. [PMID: 31965564 DOI: 10.1111/jnc.14968] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 01/13/2020] [Accepted: 01/14/2020] [Indexed: 12/11/2022]
Abstract
The discovery of genes involved in familial as well as sporadic forms of Parkinson disease (PD) constitutes an important milestone in understanding this disorder's pathophysiology and potential treatment. Among these genes, GBA1 is one of the most common and well-studied, but it is still unclear how mutations in GBA1 translate into an increased risk for developing PD. In this review, we provide an overview of the biochemical and structural relationship between GBA1 and PD to help understand the recent advances in the development of PD therapies intended to target this pathway.
Collapse
Affiliation(s)
- Marco Toffoli
- Department of Clinical and Movement Neurosciences, University College London Queen Square Institute of Neurology, London, UK
| | - Laura Smith
- Department of Clinical and Movement Neurosciences, University College London Queen Square Institute of Neurology, London, UK
| | - Anthony H V Schapira
- Department of Clinical and Movement Neurosciences, University College London Queen Square Institute of Neurology, London, UK
| |
Collapse
|
34
|
Souffrant MG, Yao XQ, Momin M, Hamelberg D. N-Glycosylation and Gaucher Disease Mutation Allosterically Alter Active-Site Dynamics of Acid-β-Glucosidase. ACS Catal 2020. [DOI: 10.1021/acscatal.9b04404] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
35
|
Brasil S, Pascoal C, Francisco R, dos Reis Ferreira V, A. Videira P, Valadão G. Artificial Intelligence (AI) in Rare Diseases: Is the Future Brighter? Genes (Basel) 2019; 10:genes10120978. [PMID: 31783696 PMCID: PMC6947640 DOI: 10.3390/genes10120978] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 02/06/2023] Open
Abstract
The amount of data collected and managed in (bio)medicine is ever-increasing. Thus, there is a need to rapidly and efficiently collect, analyze, and characterize all this information. Artificial intelligence (AI), with an emphasis on deep learning, holds great promise in this area and is already being successfully applied to basic research, diagnosis, drug discovery, and clinical trials. Rare diseases (RDs), which are severely underrepresented in basic and clinical research, can particularly benefit from AI technologies. Of the more than 7000 RDs described worldwide, only 5% have a treatment. The ability of AI technologies to integrate and analyze data from different sources (e.g., multi-omics, patient registries, and so on) can be used to overcome RDs’ challenges (e.g., low diagnostic rates, reduced number of patients, geographical dispersion, and so on). Ultimately, RDs’ AI-mediated knowledge could significantly boost therapy development. Presently, there are AI approaches being used in RDs and this review aims to collect and summarize these advances. A section dedicated to congenital disorders of glycosylation (CDG), a particular group of orphan RDs that can serve as a potential study model for other common diseases and RDs, has also been included.
Collapse
Affiliation(s)
- Sandra Brasil
- Portuguese Association for CDG, 2820-381 Lisboa, Portugal; (S.B.); (C.P.); (R.F.); (P.A.V.)
- CDG & Allies—Professionals and Patient Associations International Network (CDG & Allies—PPAIN), Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Lisboa, Portugal
| | - Carlota Pascoal
- Portuguese Association for CDG, 2820-381 Lisboa, Portugal; (S.B.); (C.P.); (R.F.); (P.A.V.)
- CDG & Allies—Professionals and Patient Associations International Network (CDG & Allies—PPAIN), Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Lisboa, Portugal
- UCIBIO, Departamento Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Lisboa, Portugal
| | - Rita Francisco
- Portuguese Association for CDG, 2820-381 Lisboa, Portugal; (S.B.); (C.P.); (R.F.); (P.A.V.)
- CDG & Allies—Professionals and Patient Associations International Network (CDG & Allies—PPAIN), Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Lisboa, Portugal
- UCIBIO, Departamento Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Lisboa, Portugal
| | - Vanessa dos Reis Ferreira
- Portuguese Association for CDG, 2820-381 Lisboa, Portugal; (S.B.); (C.P.); (R.F.); (P.A.V.)
- CDG & Allies—Professionals and Patient Associations International Network (CDG & Allies—PPAIN), Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Lisboa, Portugal
- Correspondence:
| | - Paula A. Videira
- Portuguese Association for CDG, 2820-381 Lisboa, Portugal; (S.B.); (C.P.); (R.F.); (P.A.V.)
- CDG & Allies—Professionals and Patient Associations International Network (CDG & Allies—PPAIN), Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Lisboa, Portugal
- UCIBIO, Departamento Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Lisboa, Portugal
| | - Gonçalo Valadão
- Instituto de Telecomunicações, 1049-001 Lisboa, Portugal;
- Departamento de Ciências e Tecnologias, Autónoma Techlab–Universidade Autónoma de Lisboa, 1169-023 Lisboa, Portugal
- Electronics, Telecommunications and Computers Engineering Department, Instituto Superior de Engenharia de Lisboa, 1959-007 Lisboa, Portugal
| |
Collapse
|
36
|
Romero R, Yuen T, New MI, Zaidi M, Haider S. Reply to Graham et al.: In silico atomistic coordinates and molecular dynamics simulation trajectories of the glucocerebrosidase-saposin C complex. Proc Natl Acad Sci U S A 2019; 116:11101-11102. [PMID: 31164477 PMCID: PMC6561302 DOI: 10.1073/pnas.1905744116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Raquel Romero
- Department of Pharmaceutical and Biological Chemistry, University College London School of Pharmacy, London WC1N 1AX, United Kingdom
| | - Tony Yuen
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Maria I New
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Mone Zaidi
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029;
| | - Shozeb Haider
- Department of Pharmaceutical and Biological Chemistry, University College London School of Pharmacy, London WC1N 1AX, United Kingdom;
| |
Collapse
|