A 3D Structural Interactome to Explore the Impact of Evolutionary Divergence, Population Variation, and Small-molecule Drugs on SARS-CoV-2-Human Protein-Protein Interactions

The recent COVID-19 pandemic has sparked a global public health crisis. Vital to the development of informed treatments for this disease is a comprehensive understanding of the molecular interactions involved in disease pathology. One lens through which we can better understand this pathology is through the network of protein-protein interactions between its viral agent, SARS-CoV-2, and its human host. For instance, increased infectivity of SARS-CoV-2 compared to SARS-CoV can be explained by rapid evolution along the interface between the Spike protein and its human receptor (ACE2) leading to increased binding affinity. Sequence divergences that modulate other protein-protein interactions may further explain differences in transmission and virulence in this novel coronavirus. To facilitate these comparisons, we combined homology-based structural modeling with the ECLAIR pipeline for interface prediction at residue resolution, and molecular docking with PyRosetta. This enabled us to compile a novel 3D structural interactome meta-analysis for the published interactome network between SARS-CoV-2 and human. This resource includes docked structures for all interactions with protein structures, enrichment analysis of variation along interfaces, predicted ΔΔG between SARS-CoV and SARS-CoV-2 variants for each interaction, predicted impact of natural human population variation on binding affinity, and a further prioritized set of drug repurposing candidates predicted to overlap with protein interfaces†. All predictions are available online† for easy access and are continually updated when new interactions are published. † Some sections of this pre-print have been redacted to comply with current bioRxiv policy restricting the dissemination of purely in silico results predicting potential therapies for SARS-CoV-2 that have not undergone thorough peer-review. The results section titled “Prioritization of Candidate Inhibitors of SARS-CoV-2-Human Interactions Through Binding Site Comparison,” Figure 4, Supplemental Table 9, and all links to our web resource have been removed. Blank headers left in place to preserve structure and item numbering. Our full manuscript will be published in an appropriate journal following peer-review.

[1]  Helen E. Parkinson,et al.  The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019 , 2018, Nucleic Acids Res..

[2]  N. Bastien,et al.  Analysis of multimerization of the SARS coronavirus nucleocapsid protein , 2004, Biochemical and Biophysical Research Communications.

[3]  C. Mantzoros,et al.  Severe obesity, increasing age and male sex are independently associated with worse in-hospital outcomes, and higher in-hospital mortality, in a cohort of patients with COVID-19 in the Bronx, New York , 2020, Metabolism.

[4]  S. Henikoff,et al.  Amino acid substitution matrices from protein blocks. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[5]  Christian Drosten,et al.  The SARS-Coronavirus-Host Interactome: Identification of Cyclophilins as Target for Pan-Coronavirus Inhibitors , 2011, PLoS pathogens.

[6]  K. Shi,et al.  Structural basis of receptor recognition by SARS-CoV-2 , 2020, Nature.

[7]  A. Barabasi,et al.  Network medicine : a network-based approach to human disease , 2010 .

[8]  C. Yoakim,et al.  Optimization and determination of the absolute configuration of a series of potent inhibitors of human papillomavirus type-11 E1-E2 protein-protein interaction: a combined medicinal chemistry, NMR and computational chemistry approach. , 2007, Bioorganic & medicinal chemistry.

[9]  Ben M. Webb,et al.  Comparative Protein Structure Modeling Using MODELLER , 2016, Current protocols in bioinformatics.

[10]  H. Wolfson,et al.  Spatial chemical conservation of hot spot interactions in protein-protein complexes , 2007, BMC Biology.

[11]  E. Holmes,et al.  A new coronavirus associated with human respiratory disease in China , 2020, Nature.

[12]  Zhiping Weng,et al.  Accelerating Protein Docking in ZDOCK Using an Advanced 3D Convolution Library , 2011, PloS one.

[13]  N. Jones,et al.  Crystal structure of a gamma-herpesvirus cyclin-cdk complex. , 2000, The EMBO journal.

[14]  Marc A. Martí-Renom,et al.  MODBASE: a database of annotated comparative protein structure models and associated resources , 2005, Nucleic Acids Res..

[15]  S. Perlman,et al.  Coronaviruses, Including Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS) , 2014, Mandell, Douglas, and Bennett's Principles and Practice of Infectious Diseases.

[16]  Jianhua Lin,et al.  Divergence measures based on the Shannon entropy , 1991, IEEE Trans. Inf. Theory.

[17]  Rob Kaptein,et al.  Structural properties of the promiscuous VP16 activation domain. , 2005, Biochemistry.

[18]  Devin K. Schweppe,et al.  Architecture of the human interactome defines protein communities and disease networks , 2017, Nature.

[19]  Ting Yu,et al.  Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study , 2020, The Lancet Respiratory Medicine.

[20]  N. Isern,et al.  Solution structure of the complex between poxvirus-encoded CC chemokine inhibitor vCCI and human MIP-1β , 2006, Proceedings of the National Academy of Sciences.

[21]  Haiyuan Yu,et al.  Three-dimensional reconstruction of protein networks provides insight into human genetic disease , 2012, Nature Biotechnology.

[22]  J. Wells,et al.  Small-molecule inhibitors of protein-protein interactions: progressing toward the reality. , 2014, Chemistry & biology.

[23]  Yuquan Wei,et al.  Mechanism of inhibition of retromer transport by the bacterial effector RidL , 2018, Proceedings of the National Academy of Sciences.

[24]  J. Smeitink,et al.  CIA30 complex I assembly factor: a candidate for human complex I deficiency? , 2002, Human Genetics.

[25]  K. To,et al.  Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan , 2020, Emerging microbes & infections.

[26]  Benjamin J. Polacco,et al.  A SARS-CoV-2 Protein Interaction Map Reveals Targets for Drug-Repurposing , 2020, Nature.

[27]  Rutger O. Vogel,et al.  Human mitochondrial complex I assembly is mediated by NDUFAF1 , 2005, The FEBS journal.

[28]  R. Ranganathan,et al.  Evolutionarily conserved pathways of energetic connectivity in protein families. , 1999, Science.

[29]  D. Baker,et al.  A simple physical model for binding energy hot spots in protein–protein complexes , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[30]  C. Blackmore,et al.  Disparities in Incidence of COVID-19 Among Underrepresented Racial/Ethnic Groups in Counties Identified as Hotspots During June 5–18, 2020 — 22 States, February–June 2020 , 2020, MMWR. Morbidity and mortality weekly report.

[31]  S. Schultz-Cherry,et al.  Metabolic Syndrome and Viral Pathogenesis: Lessons from Influenza and Coronaviruses , 2020, Journal of Virology.

[32]  Roland L. Dunbrack,et al.  The Rosetta all-atom energy function for macromolecular modeling and design , 2017, bioRxiv.

[33]  M. Vidal.  A unifying view of 21st century systems biology , 2009, FEBS letters.

[34]  J. Heitman.  Mandell, Douglas, and Bennett's Principles and Practice of Infectious Diseases , 2000 .

[35]  Yuntao Wu,et al.  Chemokine receptor CCR5 antagonist maraviroc: medicinal chemistry and clinical applications. , 2014, Current topics in medicinal chemistry.

[36]  Louise Thauvette,et al.  Inhibition of Human Papillomavirus DNA Replication by Small Molecule Antagonists of the E1-E2 Protein Interaction* , 2003, Journal of Biological Chemistry.

[37]  Mona Singh,et al.  Predicting functionally important residues from sequence conservation , 2007, Bioinform..

[38]  Neil Q. McDonald,et al.  Crystal structure of a γ‐herpesvirus cyclin–cdk complex , 2000 .

[39]  P. Aloy,et al.  Interactome3D: adding structural details to protein networks , 2013, Nature Methods.

[40]  Haiyuan Yu,et al.  Interactome INSIDER: a structural interactome browser for genomic studies , 2017, Nature Methods.

[41]  E. Chevet,et al.  Role of the early secretory pathway in SARS-CoV-2 infection , 2020, The Journal of cell biology.

[42]  H. Shu,et al.  TMED2 Potentiates Cellular IFN Responses to DNA Viruses by Reinforcing MITA Dimerization and Facilitating Its Trafficking. , 2018, Cell reports.

[43]  Chunlei Liu,et al.  ClinVar: improving access to variant interpretations and supporting evidence , 2017, Nucleic Acids Res..

[44]  J. Skehel,et al.  SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on virus evolution and furin-cleavage effects , 2020, Nature Structural & Molecular Biology.

[45]  Eugen C. Buehler,et al.  Human genome-wide RNAi screen reveals a role for nuclear pore proteins in poxvirus morphogenesis , 2013, Proceedings of the National Academy of Sciences.

[46]  Christus,et al.  A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins , 2022 .

[47]  A. Sali,et al.  The molecular sociology of the cell , 2007, Nature.

[48]  Mitchell J. Machiela,et al.  LDlink: a web-based application for exploring population-specific haplotype structure and linking correlated alleles of possible functional variants , 2015, Bioinform..

[49]  S. Perlman,et al.  Coronaviruses: An Overview of Their Replication and Pathogenesis , 2015, Methods in molecular biology.

[50]  Uma V. Mahajan,et al.  Racial demographics and COVID-19 confirmed cases and deaths: a correlational analysis of 2886 US counties , 2020, Journal of public health.

[51]  Jeffrey J. Gray,et al.  High-resolution protein-protein docking. , 2006, Current opinion in structural biology.

[52]  Yufei Shan,et al.  Tom70 mediates activation of interferon regulatory factor 3 on mitochondria , 2010, Cell Research.

[53]  P. Bork,et al.  A method and server for predicting damaging missense mutations , 2010, Nature Methods.

[54]  Kai Zhao,et al.  A pneumonia outbreak associated with a new coronavirus of probable bat origin , 2020, Nature.

[55]  P. Munroe,et al.  Greater risk of severe COVID-19 in Black, Asian and Minority Ethnic populations is not explained by cardiometabolic, socioeconomic or behavioural factors, or by 25(OH)-vitamin D status: study of 1326 cases from the UK Biobank , 2020, Journal of public health.

[56]  Mainak Guharoy,et al.  Conserved residue clusters at protein-protein interfaces and their use in binding site identification , 2010, BMC Bioinformatics.

[57]  Robyn M. Kaake,et al.  Protein Interaction Mapping Identifies RBBP6 as a Negative Regulator of Ebola Virus Replication , 2018, Cell.

[58]  N. Krogan,et al.  The Landscape of Human Cancer Proteins Targeted by SARS-CoV-2 , 2020, Cancer discovery.

[59]  C. Klemke,et al.  Mitochondrial Reactive Oxygen Species Control T Cell Activation by Regulating IL-2 and IL-4 Expression: Mechanism of Ciprofloxacin-Mediated Immunosuppression , 2010, The Journal of Immunology.

[60]  Sergey Lyskov,et al.  PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta , 2010, Bioinform..

[61]  P. Stenson,et al.  Human Gene Mutation Database (HGMD®): 2003 update , 2003, Human mutation.

[62]  John H. Morris,et al.  Global landscape of HIV–human protein complexes , 2011, Nature.

[63]  A. Lipovsky,et al.  Genome-wide siRNA screen identifies the retromer as a cellular entry factor for human papillomavirus , 2013, Proceedings of the National Academy of Sciences.

[64]  B. Lee,et al.  The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.

[66]  F. Cunningham,et al.  The Ensembl Variant Effect Predictor , 2016, Genome Biology.

[67]  Shayne D. Wierbowski,et al.  Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations , 2019, Nature Communications.

[68]  The UniProt Consortium,et al.  UniProt: a worldwide hub of protein knowledge , 2018, Nucleic Acids Res..

[69]  Caroline C. Friedel,et al.  Analysis of Intraviral Protein-Protein Interactions of the SARS Coronavirus ORFeome , 2007, PloS one.

[70]  B. Graham,et al.  Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation , 2020, Science.

[71]  Alice C Hughes,et al.  A Novel Bat Coronavirus Closely Related to SARS-CoV-2 Contains Natural Insertions at the S1/S2 Cleavage Site of the Spike Protein , 2020, Current Biology.

[72]  J. Xiang,et al.  Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study , 2020, The Lancet.

[73]  N. Warner,et al.  A Genome-wide Small Interfering RNA (siRNA) Screen Reveals Nuclear Factor-κB (NF-κB)-independent Regulators of NOD2-induced Interleukin-8 (IL-8) Secretion* , 2014, The Journal of Biological Chemistry.

[74]  Jing Hu,et al.  SIFT web server: predicting effects of amino acid substitutions on proteins , 2012, Nucleic Acids Res..

[75]  K. Yuen,et al.  Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2 , 2020, Cell.

[76]  Priya S. Shah,et al.  Comparative Flavivirus-Host Protein Interaction Mapping Reveals Mechanisms of Dengue and Zika Virus Pathogenesis , 2018, Cell.

[77]  E. Procko.  The sequence of human ACE2 is suboptimal for binding the S spike protein of SARS coronavirus 2 , 2020, bioRxiv.

[78]  D. Scott,et al.  Small molecules, big targets: drug discovery faces the protein–protein interaction challenge , 2016, Nature Reviews Drug Discovery.

[79]  István A. Kovács,et al.  Widespread Macromolecular Interaction Perturbations in Human Genetic Disorders , 2015, Cell.

[80]  J. Carcillo,et al.  SARS-CoV2 (COVID-19) Structural/Evolution Dynamicome: Insights into functional evolution and human genomics , 2020, bioRxiv.

[81]  David Ryan Koes,et al.  Lessons Learned in Empirical Scoring with smina from the CSAR 2011 Benchmarking Exercise , 2013, J. Chem. Inf. Model..

[82]  Cheng Wang,et al.  AlphaSpace: Fragment-Centric Topographical Mapping To Target Protein–Protein Interaction Interfaces , 2015, J. Chem. Inf. Model..

[83]  Ryan L. Collins,et al.  The mutational constraint spectrum quantified from variation in 141,456 humans , 2020, Nature.

[84]  J. Schuurs-Hoeijmakers,et al.  Presence of Genetic Variants Among Young Men With Severe COVID-19. , 2020, JAMA.

[85]  Marc L. Mendillo,et al.  The Master Regulator of the Cellular Stress Response (HSF1) Is Critical for Orthopoxvirus Infection , 2014, PLoS pathogens.

[86]  Shengqing Wan,et al.  Comparative genetic analysis of the novel coronavirus (2019-nCoV/SARS-CoV-2) receptor ACE2 in different populations , 2020, Cell Discovery.

[87]  Terence Hwa,et al.  Direct coupling analysis for protein contact prediction. , 2014, Methods in molecular biology.

[88]  H. Krumholz,et al.  Extrapulmonary manifestations of COVID-19 , 2020, Nature Medicine.

[89]  John W. Pinney,et al.  Protein–Protein Interactions in Virus–Host Systems , 2017, Front. Microbiol..

[90]  Magdalena Szumilas.  Explaining odds ratios. , 2010, Journal of the Canadian Academy of Child and Adolescent Psychiatry = Journal de l'Academie canadienne de psychiatrie de l'enfant et de l'adolescent.

[91]  Yan Zhao,et al.  Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China. , 2020, JAMA.

[92]  Chris Morley,et al.  Open Babel: An open chemical toolbox , 2011, J. Cheminformatics.

[93]  P. Adab,et al.  Who is most likely to be infected with SARS-CoV-2? , 2020, The Lancet Infectious Diseases.

[94]  Joseph Rosenbluh,et al.  Inhibiting HIV-1 integrase by shifting its oligomerization equilibrium , 2007, Proceedings of the National Academy of Sciences.

[95]  R D Appel,et al.  Protein identification and analysis tools in the ExPASy server. , 1999, Methods in molecular biology.

[96]  Thomas S. Peat,et al.  Small Molecule Inhibitors of the LEDGF Site of Human Immunodeficiency Virus Integrase Identified by Fragment Screening and Structure Based Design , 2012, PloS one.

[97]  Beau B. Bruce,et al.  Characteristics Associated with Hospitalization Among Patients with COVID-19 — Metropolitan Atlanta, Georgia, March–April 2020 , 2020, MMWR. Morbidity and mortality weekly report.

[98]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[99]  M. Maginnis.  Virus–Receptor Interactions: The Key to Cellular Invasion , 2018, Journal of Molecular Biology.

[100]  Jacques Fellay,et al.  A Whole-Genome Association Study of Major Determinants for Host Control of HIV-1 , 2007, Science.

[101]  Gaël Varoquaux,et al.  Scikit-learn: Machine Learning in Python , 2011, J. Mach. Learn. Res..

[102]  James W. Noah,et al.  Identification of Protein-Protein Interaction Inhibitors Targeting Vaccinia Virus Processivity Factor for Development of Antiviral Agents , 2011, Antimicrobial Agents and Chemotherapy.

[103]  N. Rezaei,et al.  Genetic predisposition models to COVID-19 infection , 2020, Medical Hypotheses.

[104]  Daniel Wrapp,et al.  Stabilized coronavirus spikes are resistant to conformational changes induced by receptor recognition or proteolysis , 2018, Scientific Reports.

[105]  M. Davids,et al.  The Development and Current Use of BCL-2 Inhibitors for the Treatment of Chronic Lymphocytic Leukemia , 2017, Current Hematologic Malignancy Reports.

[106]  G. Herrler,et al.  SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor , 2020, Cell.

[107]  E. Gherardi,et al.  Structure of the Human Receptor Tyrosine Kinase Met in Complex with the Listeria Invasion Protein InlB , 2007, Cell.

[108]  Rui Ji,et al.  Prevalence of comorbidities and its effects in patients infected with SARS-CoV-2: a systematic review and meta-analysis , 2020, International Journal of Infectious Diseases.

[109]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[110]  A. Mesecar,et al.  Structural Insights into the Interaction of Coronavirus Papain-Like Proteases and Interferon-Stimulated Gene Product 15 from Different Species , 2017, Journal of Molecular Biology.

[111]  A. Walls,et al.  Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein , 2020, Cell.