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Monsia R, Bhattacharyya S. Virtual Screening of Molecules via Neural Fingerprint-based Deep Learning Technique. RESEARCH SQUARE 2024:rs.3.rs-4355625. [PMID: 38766198 PMCID: PMC11100899 DOI: 10.21203/rs.3.rs-4355625/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
A machine learning-based drug screening technique has been developed and optimized using convolutional neural network-derived fingerprints. The optimization of weights in the neural network-based fingerprinting technique was compared with fixed Morgan fingerprints in regard to binary classification on drug-target binding affinity. The assessment was carried out using six different target proteins using randomly chosen small molecules from the ZINC15 database for training. This new architecture proved to be more efficient in screening molecules that less favorably bind to specific targets and retaining molecules that favorably bind to it. Scientific contribution We have developed a new neural fingerprint-based screening model that has a significant ability to capture hits. Despite using a smaller dataset, this model is capable of mapping chemical space similar to other contemporary algorithms designed for molecular screening. The novelty of the present algorithm lies in the speed with which the models are trained and tuned before testing its predictive capabilities and hence is a significant step forward in the field of machine learning-embedded computational drug discovery.
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2
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Tangos M, Jarkas M, Akin I, El-Battrawy I, Hamdani N. Cardiac damage and tropism of severe acute respiratory syndrome coronavirus 2. Curr Opin Microbiol 2024; 78:102437. [PMID: 38394964 DOI: 10.1016/j.mib.2024.102437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024]
Abstract
Until now, the World Health Organization registered over 771 million cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection worldwide, of which 6.97 million resulted in death. Virus-related cardiovascular events and pre-existing heart problems have been identified as major contributing factors to global infection-related morbidity and mortality, emphasizing the necessity for risk assessment and future prevention. In this review, we highlight cardiac manifestations that might arise from an infection with SARS-CoV-2 and provide an overview of known comorbidities that worsen the outcome. Additionally, we aim to summarize the therapeutic strategies proposed to reverse virus-associated myocardial damage, which will be further highlighted in this review, with an outlook to successful recovery and prevention.
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Affiliation(s)
- Melina Tangos
- Institute of Physiology, Department of Cellular and Translational Physiology, Medical Faculty, Ruhr University Bochum, Bochum, Germany; Institut für Forschung und Lehre (IFL), Molecular and Experimental Cardiology, Ruhr University Bochum, Bochum, Germany; Department of Cardiology, St. Josef-Hospital of the Ruhr University Bochum, Bochum, Germany
| | - Muhammad Jarkas
- Institute of Physiology, Department of Cellular and Translational Physiology, Medical Faculty, Ruhr University Bochum, Bochum, Germany; Institut für Forschung und Lehre (IFL), Molecular and Experimental Cardiology, Ruhr University Bochum, Bochum, Germany; Department of Cardiology, St. Josef-Hospital of the Ruhr University Bochum, Bochum, Germany
| | - Ibrahim Akin
- First Department of Medicine, University Medical Centre Mannheim (UMM), Mannheim, Germany
| | - Ibrahim El-Battrawy
- Institute of Physiology, Department of Cellular and Translational Physiology, Medical Faculty, Ruhr University Bochum, Bochum, Germany; Institut für Forschung und Lehre (IFL), Molecular and Experimental Cardiology, Ruhr University Bochum, Bochum, Germany; Department of Cardiology and Angiology, Bergmannsheil University Hospital, Ruhr University Bochum, Bochum, Germany
| | - Nazha Hamdani
- Institute of Physiology, Department of Cellular and Translational Physiology, Medical Faculty, Ruhr University Bochum, Bochum, Germany; Institut für Forschung und Lehre (IFL), Molecular and Experimental Cardiology, Ruhr University Bochum, Bochum, Germany; Department of Cardiology, St. Josef-Hospital of the Ruhr University Bochum, Bochum, Germany; HCEMM-SU Cardiovascular Comorbidities Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1089 Budapest, Hungary; Department of Physiology, Cardiovascular Research Institute Maastricht University Maastricht, Maastricht, the Netherlands.
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3
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Grand RJ. SARS-CoV-2 and the DNA damage response. J Gen Virol 2023; 104:001918. [PMID: 37948194 PMCID: PMC10768691 DOI: 10.1099/jgv.0.001918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023] Open
Abstract
The recent coronavirus disease 2019 (COVID-19) pandemic was caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 is characterized by respiratory distress, multiorgan dysfunction and, in some cases, death. The virus is also responsible for post-COVID-19 condition (commonly referred to as 'long COVID'). SARS-CoV-2 is a single-stranded, positive-sense RNA virus with a genome of approximately 30 kb, which encodes 26 proteins. It has been reported to affect multiple pathways in infected cells, resulting, in many cases, in the induction of a 'cytokine storm' and cellular senescence. Perhaps because it is an RNA virus, replicating largely in the cytoplasm, the effect of SARS-Cov-2 on genome stability and DNA damage responses (DDRs) has received relatively little attention. However, it is now becoming clear that the virus causes damage to cellular DNA, as shown by the presence of micronuclei, DNA repair foci and increased comet tails in infected cells. This review considers recent evidence indicating how SARS-CoV-2 causes genome instability, deregulates the cell cycle and targets specific components of DDR pathways. The significance of the virus's ability to cause cellular senescence is also considered, as are the implications of genome instability for patients suffering from long COVID.
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Affiliation(s)
- Roger J. Grand
- Institute for Cancer and Genomic Science, The Medical School, University of Birmingham, Birmingham, UK
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4
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Saleh MG, Chang L, Liang H, Ryan MC, Cunningham E, Garner J, Wilson E, Levine AR, Kottilil S, Ernst T. Ongoing oxidative stress in individuals with post-acute sequelae of COVID-19. NEUROIMMUNE PHARMACOLOGY AND THERAPEUTICS 2023; 2:89-94. [PMID: 37476292 PMCID: PMC10355326 DOI: 10.1515/nipt-2022-0006] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 07/22/2023]
Abstract
Objectives Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 infection is associated with lower plasma glutathione (GSH) levels due to oxidative stress. However, plasma levels may not reflect brain GSH levels. Individuals with post-acute sequelae of COVID-19 (PASC) have a higher prevalence of cognitive fatigue, which might be related to altered brain γ-aminobutyric-acid (GABA) levels. Hence, our study aims to measure the brain GSH and GABA levels in PASC. Methods 29 PASC participants and 24 uninfected controls were recruited for this study. Each was evaluated with detailed neuropsychiatric assessments and an edited proton MRS (Hadamard Encoding and Reconstruction of Mega-Edited Spectroscopy, HERMES) method to measure GABA and GSH concentrations in predominantly grey matter (GM) and predominantly white matter (WM) brain frontal voxels. Results PASC participants were 219 ± 137 days since their COVID-19 diagnosis. Nine individuals with PASC were hospitalized. Compared to controls, individuals with PASC had similar levels of GABA in both brain regions, but lower GSH and greater age-related GSH decline in the frontal GM region. Conclusions The lower-than-normal frontal GM GSH level in participants with PASC suggest that they have ongoing oxidative stress in the brain, and that older individuals may be even more vulnerable to oxidative stress.
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Affiliation(s)
- Muhammad G. Saleh
- Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Linda Chang
- Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Neurology, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Huajun Liang
- Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Meghann C. Ryan
- Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Eric Cunningham
- Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jonathan Garner
- Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Eleanor Wilson
- Department of Medicine, Division of Infectious Disease, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Andrea R. Levine
- Division of Pulmonary & Critical Care Medicine, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Shyamasundaran Kottilil
- Department of Medicine, Division of Infectious Disease, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Thomas Ernst
- Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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5
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Yao Z, Geng B, Marcon E, Pu S, Tang H, Merluza J, Bello A, Snider J, Lu P, Wood H, Stagljar I. Omicron Spike Protein Is Vulnerable to Reduction. J Mol Biol 2023; 435:168128. [PMID: 37100168 PMCID: PMC10125213 DOI: 10.1016/j.jmb.2023.168128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/10/2023] [Accepted: 04/18/2023] [Indexed: 04/28/2023]
Abstract
SARS-CoV-2 virus spike (S) protein is an envelope protein responsible for binding to the ACE2 receptor, driving subsequent entry into host cells. The existence of multiple disulfide bonds in the S protein makes it potentially susceptible to reductive cleavage. Using a tri-part split luciferase-based binding assay, we evaluated the impacts of chemical reduction on S proteins from different virus variants and found that those from the Omicron family are highly vulnerable to reduction. Through manipulation of different Omicron mutations, we found that alterations in the receptor binding module (RBM) are the major determinants of this vulnerability. Specifically we discovered that Omicron mutations facilitate the cleavage of C480-C488 and C379-C432 disulfides, which consequently impairs binding activity and protein stability. The vulnerability of Omicron S proteins suggests a mechanism that can be harnessed to treat specific SARS-CoV-2 strains.
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Affiliation(s)
- Zhong Yao
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 3E1, Canada.
| | - Betty Geng
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Edyta Marcon
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Shuye Pu
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Hua Tang
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - John Merluza
- Zoonotic Diseases and Special Pathogens division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | - Alexander Bello
- Zoonotic Diseases and Special Pathogens division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | - Jamie Snider
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Ping Lu
- Department of Vascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Heidi Wood
- Zoonotic Diseases and Special Pathogens division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | - Igor Stagljar
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada; Mediterranean Institute for Life Sciences, Meštrovićevo Šetalište 45, HR-21000 Split, Croatia.
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6
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Enichen E, Harvey C, Demmig-Adams B. COVID-19 Spotlights Connections between Disease and Multiple Lifestyle Factors. Am J Lifestyle Med 2023; 17:231-257. [PMID: 36883129 PMCID: PMC9445631 DOI: 10.1177/15598276221123005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The SARS-CoV-2 virus (severe acute respiratory syndrome coronavirus 2), and the disease it causes (COVID-19), have had a profound impact on global human society and threaten to continue to have such an impact with newly emerging variants. Because of the widespread effects of SARS-CoV-2, understanding how lifestyle choices impact the severity of disease is imperative. This review summarizes evidence for an involvement of chronic, non-resolving inflammation, gut microbiome disruption (dysbiosis with loss of beneficial microorganisms), and impaired viral defenses, all of which are associated with an imbalanced lifestyle, in severe disease manifestations and post-acute sequelae of SARS-CoV-2 (PASC). Humans' physiological propensity for uncontrolled inflammation and severe COVID-19 are briefly contrasted with bats' low propensity for inflammation and their resistance to viral disease. This insight is used to identify positive lifestyle factors with the potential to act in synergy for restoring balance to the immune response and gut microbiome, and thereby protect individuals against severe COVID-19 and PASC. It is proposed that clinicians should consider recommending lifestyle factors, such as stress management, balanced nutrition and physical activity, as preventative measures against severe viral disease and PASC.
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Affiliation(s)
- Elizabeth Enichen
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA (EE, CH, BDA)
| | - Caitlyn Harvey
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA (EE, CH, BDA)
| | - Barbara Demmig-Adams
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA (EE, CH, BDA)
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7
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Pisoschi AM, Iordache F, Stanca L, Gajaila I, Ghimpeteanu OM, Geicu OI, Bilteanu L, Serban AI. Antioxidant, Anti-inflammatory, and Immunomodulatory Roles of Nonvitamin Antioxidants in Anti-SARS-CoV-2 Therapy. J Med Chem 2022; 65:12562-12593. [PMID: 36136726 PMCID: PMC9514372 DOI: 10.1021/acs.jmedchem.2c01134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Indexed: 11/28/2022]
Abstract
Viral pathologies encompass activation of pro-oxidative pathways and inflammatory burst. Alleviating overproduction of reactive oxygen species and cytokine storm in COVID-19 is essential to counteract the immunogenic damage in endothelium and alveolar membranes. Antioxidants alleviate oxidative stress, cytokine storm, hyperinflammation, and diminish the risk of organ failure. Direct antiviral roles imply: impact on viral spike protein, interference with the ACE2 receptor, inhibition of dipeptidyl peptidase 4, transmembrane protease serine 2 or furin, and impact on of helicase, papain-like protease, 3-chyomotrypsin like protease, and RNA-dependent RNA polymerase. Prooxidative environment favors conformational changes in the receptor binding domain, promoting the affinity of the spike protein for the host receptor. Viral pathologies imply a vicious cycle, oxidative stress promoting inflammatory responses, and vice versa. The same was noticed with respect to the relationship antioxidant impairment-viral replication. Timing, dosage, pro-oxidative activities, mutual influences, and interference with other antioxidants should be carefully regarded. Deficiency is linked to illness severity.
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Affiliation(s)
- Aurelia Magdalena Pisoschi
- Faculty of Veterinary Medicine, Department Preclinical
Sciences, University of Agronomic Sciences and Veterinary Medicine of
Bucharest, 105 Splaiul Independentei, 050097Bucharest,
Romania
| | - Florin Iordache
- Faculty of Veterinary Medicine, Department Preclinical
Sciences, University of Agronomic Sciences and Veterinary Medicine of
Bucharest, 105 Splaiul Independentei, 050097Bucharest,
Romania
| | - Loredana Stanca
- Faculty of Veterinary Medicine, Department Preclinical
Sciences, University of Agronomic Sciences and Veterinary Medicine of
Bucharest, 105 Splaiul Independentei, 050097Bucharest,
Romania
| | - Iuliana Gajaila
- Faculty of Veterinary Medicine, Department Preclinical
Sciences, University of Agronomic Sciences and Veterinary Medicine of
Bucharest, 105 Splaiul Independentei, 050097Bucharest,
Romania
| | - Oana Margarita Ghimpeteanu
- Faculty of Veterinary Medicine, Department Preclinical
Sciences, University of Agronomic Sciences and Veterinary Medicine of
Bucharest, 105 Splaiul Independentei, 050097Bucharest,
Romania
| | - Ovidiu Ionut Geicu
- Faculty of Veterinary Medicine, Department Preclinical
Sciences, University of Agronomic Sciences and Veterinary Medicine of
Bucharest, 105 Splaiul Independentei, 050097Bucharest,
Romania
- Faculty of Biology, Department Biochemistry and
Molecular Biology, University of Bucharest, 91-95 Splaiul
Independentei, 050095Bucharest, Romania
| | - Liviu Bilteanu
- Faculty of Veterinary Medicine, Department Preclinical
Sciences, University of Agronomic Sciences and Veterinary Medicine of
Bucharest, 105 Splaiul Independentei, 050097Bucharest,
Romania
- Molecular Nanotechnology Laboratory,
National Institute for Research and Development in
Microtechnologies, 126A Erou Iancu Nicolae Street, 077190Bucharest,
Romania
| | - Andreea Iren Serban
- Faculty of Veterinary Medicine, Department Preclinical
Sciences, University of Agronomic Sciences and Veterinary Medicine of
Bucharest, 105 Splaiul Independentei, 050097Bucharest,
Romania
- Faculty of Biology, Department Biochemistry and
Molecular Biology, University of Bucharest, 91-95 Splaiul
Independentei, 050095Bucharest, Romania
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8
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Labarrere CA, Kassab GS. Glutathione deficiency in the pathogenesis of SARS-CoV-2 infection and its effects upon the host immune response in severe COVID-19 disease. Front Microbiol 2022; 13:979719. [PMID: 36274722 PMCID: PMC9582773 DOI: 10.3389/fmicb.2022.979719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/14/2022] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes coronavirus disease 19 (COVID-19) has numerous risk factors leading to severe disease with high mortality rate. Oxidative stress with excessive production of reactive oxygen species (ROS) that lower glutathione (GSH) levels seems to be a common pathway associated with the high COVID-19 mortality. GSH is a unique small but powerful molecule paramount for life. It sustains adequate redox cell signaling since a physiologic level of oxidative stress is fundamental for controlling life processes via redox signaling, but excessive oxidation causes cell and tissue damage. The water-soluble GSH tripeptide (γ-L-glutamyl-L-cysteinyl-glycine) is present in the cytoplasm of all cells. GSH is at 1–10 mM concentrations in all mammalian tissues (highest concentration in liver) as the most abundant non-protein thiol that protects against excessive oxidative stress. Oxidative stress also activates the Kelch-like ECH-associated protein 1 (Keap1)-Nuclear factor erythroid 2-related factor 2 (Nrf2)-antioxidant response element (ARE) redox regulator pathway, releasing Nrf2 to regulate the expression of genes that control antioxidant, inflammatory and immune system responses, facilitating GSH activity. GSH exists in the thiol-reduced and disulfide-oxidized (GSSG) forms. Reduced GSH is the prevailing form accounting for >98% of total GSH. The concentrations of GSH and GSSG and their molar ratio are indicators of the functionality of the cell and its alteration is related to various human pathological processes including COVID-19. Oxidative stress plays a prominent role in SARS-CoV-2 infection following recognition of the viral S-protein by angiotensin converting enzyme-2 receptor and pattern recognition receptors like toll-like receptors 2 and 4, and activation of transcription factors like nuclear factor kappa B, that subsequently activate nicotinamide adenine dinucleotide phosphate (NADPH) oxidase (NOX) expression succeeded by ROS production. GSH depletion may have a fundamental role in COVID-19 pathophysiology, host immune response and disease severity and mortality. Therapies enhancing GSH could become a cornerstone to reduce severity and fatal outcomes of COVID-19 disease and increasing GSH levels may prevent and subdue the disease. The life value of GSH makes for a paramount research field in biology and medicine and may be key against SARS-CoV-2 infection and COVID-19 disease.
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9
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Wozney AJ, Smith MA, Abdrabbo M, Birch CM, Cicigoi KA, Dolan CC, Gerzema AEL, Hansen A, Henseler EJ, LaBerge B, Leavens CM, Le CN, Lindquist AC, Ludwig RK, O'Reilly MG, Reynolds JH, Sherman BA, Sillman HW, Smith MA, Snortheim MJ, Svaren LM, Vanderpas EC, Voon A, Wackett MJ, Weiss MM, Hati S, Bhattacharyya S. Evolution of Stronger SARS-CoV-2 Variants as Revealed Through the Lens of Molecular Dynamics Simulations. Protein J 2022; 41:444-456. [PMID: 35913554 PMCID: PMC9340756 DOI: 10.1007/s10930-022-10065-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/27/2022] [Indexed: 12/03/2022]
Abstract
Using molecular dynamics simulations, the protein–protein interactions of the receptor-binding domain of the wild-type and seven variants of the severe acute respiratory syndrome coronavirus 2 spike protein and the peptidase domain of human angiotensin-converting enzyme 2 were investigated. These variants are alpha, beta, gamma, delta, eta, kappa, and omicron. Using 100 ns simulation data, the residue interaction networks at the protein–protein interface were identified. Also, the impact of mutations on essential protein dynamics, backbone flexibility, and interaction energy of the simulated protein–protein complexes were studied. The protein–protein interface for the wild-type, delta, and omicron variants contained several stronger interactions, while the alpha, beta, gamma, eta, and kappa variants exhibited an opposite scenario as evident from the analysis of the inter-residue interaction distances and pair-wise interaction energies. The study reveals that two distinct residue networks at the central and right contact regions forge stronger binding affinity between the protein partners. The study provides a molecular-level insight into how enhanced transmissibility and infectivity by delta and omicron variants are most likely tied to a handful of interacting residues at the binding interface, which could potentially be utilized for future antibody constructs and structure-based antiviral drug design.
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Affiliation(s)
- Alec J Wozney
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Macey A Smith
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Mobeen Abdrabbo
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Cole M Birch
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Kelsey A Cicigoi
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Connor C Dolan
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Audrey E L Gerzema
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Abby Hansen
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Ethan J Henseler
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Ben LaBerge
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Caterra M Leavens
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Christine N Le
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Allison C Lindquist
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Rikaela K Ludwig
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Maggie G O'Reilly
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Jacob H Reynolds
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Brandon A Sherman
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Hunter W Sillman
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Michael A Smith
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Marissa J Snortheim
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Levi M Svaren
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Emily C Vanderpas
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Aidan Voon
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Miles J Wackett
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Moriah M Weiss
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Sanchita Hati
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA.
| | - Sudeep Bhattacharyya
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA.
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10
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Gao K, Wang R, Chen J, Cheng L, Frishcosy J, Huzumi Y, Qiu Y, Schluckbier T, Wei X, Wei GW. Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. Chem Rev 2022; 122:11287-11368. [PMID: 35594413 PMCID: PMC9159519 DOI: 10.1021/acs.chemrev.1c00965] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.
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Affiliation(s)
- Kaifu Gao
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Rui Wang
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiahui Chen
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Limei Cheng
- Clinical
Pharmacology and Pharmacometrics, Bristol
Myers Squibb, Princeton, New Jersey 08536, United States
| | - Jaclyn Frishcosy
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuta Huzumi
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuchi Qiu
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tom Schluckbier
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Xiaoqi Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Guo-Wei Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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