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Wang Z, Belecciu T, Eaves J, Reimers M, Bachmann MH, Woldring D. Phytochemical drug discovery for COVID-19 using high-resolution computational docking and machine learning assisted binder prediction. J Biomol Struct Dyn 2022:1-21. [PMID: 35993534 DOI: 10.1080/07391102.2022.2112976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
The COVID-19 pandemic has resulted in millions of deaths around the world. Multiple vaccines are in use, but there are many underserved locations that do not have adequate access to them. Variants may emerge that are highly resistant to existing vaccines, and therefore cheap and readily obtainable therapeutics are needed. Phytochemicals, or plant chemicals, can possibly be such therapeutics. Phytochemicals can be used in a polypharmacological approach, where multiple viral proteins are inhibited and escape mutations are made less likely. Finding the right phytochemicals for viral protein inhibition is challenging, but in-silico screening methods can make this a more tractable problem. In this study, we screen a wide range of natural drug products against a comprehensive set of SARS-CoV-2 proteins using a high-resolution computational workflow. This workflow consists of a structure-based virtual screening (SBVS), where an initial phytochemical library was docked against all selected protein structures. Subsequently, ligand-based virtual screening (LBVS) was employed, where chemical features of 34 lead compounds obtained from the SBVS were used to predict 53 lead compounds from a larger phytochemical library via supervised learning. A computational docking validation of the 53 predicted leads obtained from LBVS revealed that 28 of them elicit strong binding interactions with SARS-CoV-2 proteins. Thus, the inclusion of LBVS resulted in a 4-fold increase in the lead discovery rate. Of the total 62 leads, 18 showed promising pharmacokinetic properties in a computational ADME screening. Collectively, this study demonstrates the advantage of incorporating machine learning elements into a virtual screening workflow.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zirui Wang
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA.,Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
| | - Theodore Belecciu
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA.,Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
| | - Joelle Eaves
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA.,Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
| | - Mark Reimers
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA.,Department of Biomedical Engineering, Michigan State University, East Lansing, MI, USA
| | - Michael H Bachmann
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA.,Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Daniel Woldring
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA.,Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
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Beyond emotion: online takeaway food consumption is associated with emotional overeating among Chinese college students. Eat Weight Disord 2022; 27:781-790. [PMID: 34052988 DOI: 10.1007/s40519-021-01224-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 05/20/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Online takeaway food has become very popular in China. However, the potential effects of online takeaway food consumption on eating behaviours among individuals during the transition stage from adolescence to young adulthood have not yet been assessed. OBJECTIVE This study aimed to examine the effects of takeaway food consumption on emotional overeating behaviour among college students. METHODS Data were collected from 1450 college students from six universities in Anhui, China. The frequency of emotional overeating during the past 4 weeks was assessed by the emotional overeating questionnaire (EOQ). Data on the frequency of online takeaway food consumption and other potential risk factors at the individual, interpersonal, physical environment, and macro-system levels were assessed by questionnaire. Multilevel linear regression analyses were employed to explore the association between takeaway food consumption and emotional overeating behaviour. RESULTS Compared to those who consumed online takeaway food less than 1 day per week, participants who consumed this food 4-5 days per week and participants who consumed this food 6-7 days per week had significantly higher EOQ scores (β = 0.14, p < 0.05 and β = 0.67, p < 0.001, respectively). More frequent consumption was associated with higher EOQ scores (p for trend < 0.001). CONCLUSION A higher frequency of takeaway food consumption was associated with an elevated risk of emotional overeating among college students independent of personal emotional status and other potential confounders at the interpersonal, physical environmental and macro-system levels. LEVEL OF EVIDENCE Level V; cross-sectional descriptive study.
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Perico L, Benigni A, Casiraghi F, Ng LFP, Renia L, Remuzzi G. Immunity, endothelial injury and complement-induced coagulopathy in COVID-19. Nat Rev Nephrol 2021; 17:46-64. [PMID: 33077917 PMCID: PMC7570423 DOI: 10.1038/s41581-020-00357-4] [Citation(s) in RCA: 341] [Impact Index Per Article: 113.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/18/2020] [Indexed: 01/08/2023]
Abstract
In December 2019, a novel coronavirus was isolated from the respiratory epithelium of patients with unexplained pneumonia in Wuhan, China. This pathogen, named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causes a pathogenic condition that has been termed coronavirus disease 2019 (COVID-19) and has reached pandemic proportions. As of 17 September 2020, more than 30 million confirmed SARS-CoV-2 infections have been reported in 204 different countries, claiming more than 1 million lives worldwide. Accumulating evidence suggests that SARS-CoV-2 infection can lead to a variety of clinical conditions, ranging from asymptomatic to life-threatening cases. In the early stages of the disease, most patients experience mild clinical symptoms, including a high fever and dry cough. However, 20% of patients rapidly progress to severe illness characterized by atypical interstitial bilateral pneumonia, acute respiratory distress syndrome and multiorgan dysfunction. Almost 10% of these critically ill patients subsequently die. Insights into the pathogenic mechanisms underlying SARS-CoV-2 infection and COVID-19 progression are emerging and highlight the critical role of the immunological hyper-response - characterized by widespread endothelial damage, complement-induced blood clotting and systemic microangiopathy - in disease exacerbation. These insights may aid the identification of new or existing therapeutic interventions to limit the progression of early disease and treat severe cases.
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Affiliation(s)
- Luca Perico
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
| | - Ariela Benigni
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
| | | | - Lisa F P Ng
- Infectious Diseases Horizontal Technology Centre (ID HTC), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Laurent Renia
- Infectious Diseases Horizontal Technology Centre (ID HTC), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Giuseppe Remuzzi
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy.
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy.
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Whitfield TW, Ragland DA, Zeldovich KB, Schiffer CA. Characterizing Protein-Ligand Binding Using Atomistic Simulation and Machine Learning: Application to Drug Resistance in HIV-1 Protease. J Chem Theory Comput 2020; 16:1284-1299. [PMID: 31877249 DOI: 10.1021/acs.jctc.9b00781] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Over the past several decades, atomistic simulations of biomolecules, whether carried out using molecular dynamics or Monte Carlo techniques, have provided detailed insights into their function. Comparing the results of such simulations for a few closely related systems has guided our understanding of the mechanisms by which changes such as ligand binding or mutation can alter the function. The general problem of detecting and interpreting such mechanisms from simulations of many related systems, however, remains a challenge. This problem is addressed here by applying supervised and unsupervised machine learning techniques to a variety of thermodynamic observables extracted from molecular dynamics simulations of different systems. As an important test case, these methods are applied to understand the evasion by human immunodeficiency virus type-1 (HIV-1) protease of darunavir, a potent inhibitor to which resistance can develop via the simultaneous mutation of multiple amino acids. Complex mutational patterns have been observed among resistant strains, presenting a challenge to developing a mechanistic picture of resistance in the protease. In order to dissect these patterns and gain mechanistic insight into the role of specific mutations, molecular dynamics simulations were carried out on a collection of HIV-1 protease variants, chosen to include highly resistant strains and susceptible controls, in complex with darunavir. Using a machine learning approach that takes advantage of the hierarchical nature in the relationships among the sequence, structure, and function, an integrative analysis of these trajectories reveals key details of the resistance mechanism, including changes in the protein structure, hydrogen bonding, and protein-ligand contacts.
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Affiliation(s)
- Troy W Whitfield
- Department of Medicine , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States.,Program in Bioinformatics and Integrative Biology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States
| | - Debra A Ragland
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States
| | - Konstantin B Zeldovich
- Program in Bioinformatics and Integrative Biology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States
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Majewski M, Ruiz-Carmona S, Barril X. An investigation of structural stability in protein-ligand complexes reveals the balance between order and disorder. Commun Chem 2019. [DOI: 10.1038/s42004-019-0205-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Abstract
The predominant view in structure-based drug design is that small-molecule ligands, once bound to their target structures, display a well-defined binding mode. However, structural stability (robustness) is not necessary for thermodynamic stability (binding affinity). In fact, it entails an entropic penalty that counters complex formation. Surprisingly, little is known about the causes, consequences and real degree of robustness of protein-ligand complexes. Since hydrogen bonds have been described as essential for structural stability, here we investigate 469 such interactions across two diverse structure sets, comprising of 79 drug-like and 27 fragment ligands, respectively. Completely constricted protein-ligand complexes are rare and may fulfill a functional role. Most complexes balance order and disorder by combining a single anchoring point with looser regions. 25% do not contain any robust hydrogen bond and may form loose structures. Structural stability analysis reveals a hidden layer of complexity in protein-ligand complexes that should be considered in ligand design.
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Cao Y, Sun Y, Karimi M, Chen H, Moronfoye O, Shen Y. Predicting pathogenicity of missense variants with weakly supervised regression. Hum Mutat 2019; 40:1579-1592. [PMID: 31144781 PMCID: PMC6744350 DOI: 10.1002/humu.23826] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/23/2019] [Accepted: 05/27/2019] [Indexed: 12/27/2022]
Abstract
Quickly growing genetic variation data of unknown clinical significance demand computational methods that can reliably predict clinical phenotypes and deeply unravel molecular mechanisms. On the platform enabled by the Critical Assessment of Genome Interpretation (CAGI), we develop a novel "weakly supervised" regression (WSR) model that not only predicts precise clinical significance (probability of pathogenicity) from inexact training annotations (class of pathogenicity) but also infers underlying molecular mechanisms in a variant-specific manner. Compared to multiclass logistic regression, a representative multiclass classifier, our kernelized WSR improves the performance for the ENIGMA Challenge set from 0.72 to 0.97 in binary area under the receiver operating characteristic curve (AUC) and from 0.64 to 0.80 in ordinal multiclass AUC. WSR model interpretation and protein structural interpretation reach consensus in corroborating the most probable molecular mechanisms by which some pathogenic BRCA1 variants confer clinical significance, namely metal-binding disruption for p.C44F and p.C47Y, protein-binding disruption for p.M18T, and structure destabilization for p.S1715N.
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Affiliation(s)
- Yue Cao
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, 77843-3128, United States
| | - Yuanfei Sun
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, 77843-3128, United States
| | - Mostafa Karimi
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, 77843-3128, United States
| | - Haoran Chen
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, 77843-3128, United States
| | - Oluwaseyi Moronfoye
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, 77843-3128, United States
| | - Yang Shen
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, 77843-3128, United States
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Abstract
Motivation Multistate protein design addresses real-world challenges, such as multi-specificity design and backbone flexibility, by considering both positive and negative protein states with an ensemble of substates for each. It also presents an enormous challenge to exact algorithms that guarantee the optimal solutions and enable a direct test of mechanistic hypotheses behind models. However, efficient exact algorithms are lacking for multistate protein design. Results We have developed an efficient exact algorithm called interconnected cost function networks (iCFN) for multistate protein design. Its generic formulation allows for a wide array of applications such as stability, affinity and specificity designs while addressing concerns such as global flexibility of protein backbones. iCFN treats each substate design as a weighted constraint satisfaction problem (WCSP) modeled through a CFN; and it solves the coupled WCSPs using novel bounds and a depth-first branch-and-bound search over a tree structure of sequences, substates, and conformations. When iCFN is applied to specificity design of a T-cell receptor, a problem of unprecedented size to exact methods, it drastically reduces search space and running time to make the problem tractable. Moreover, iCFN generates experimentally-agreeing receptor designs with improved accuracy compared with state-of-the-art methods, highlights the importance of modeling backbone flexibility in protein design, and reveals molecular mechanisms underlying binding specificity. Availability and implementation https://shen-lab.github.io/software/iCFN. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Mostafa Karimi
- Department of Electrical and Computer Engineering and TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, USA
| | - Yang Shen
- Department of Electrical and Computer Engineering and TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, USA
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