Article
Biochemistry & Molecular Biology
Yanqiang Han, Zhilong Wang, Zhiyun Wei, Igor Schapiro, Jinjin Li
Summary: This study investigated the effects of residue mutations in the S glycoprotein of SARS-CoV-2 on binding affinity using molecular dynamics simulations and sequence analysis. The findings demonstrated varying degrees of enhancements in binding affinity for different variants, providing a basis for further research on virus mutations.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Multidisciplinary Sciences
Jordana Munoz-Basagoiti, Fabio Luis Lima Monteiro, Lauren R. H. Krumpe, Victoria Armario-Najera, Shilpa R. Shenoy, Daniel Perez-Zsolt, Harrison James Westgarth, Gemma Villorbina, Larissa Maciel Bomfim, Dalia Raich-Regue, Lara Nogueras, Curtis J. Henrich, Marcal Gallemi, Filipe Romero Rebello Moreira, Pascual Torres, Jennifer Wilson, Mirela D'arc, Silvia Marfil, Alice Laschuk Herlinger, Edwards Pradenas, Luiza Mendonca Higa, Manuel Portero-Otin, Benjamin Trinite, Richard M. Twyman, Teresa Capell, Amilcar Tanuri, Julia Blanco, Nuria Izquierdo-Useros, Elibio L. Rech, Paul Christou, Barry R. O'Keefe
Summary: SARS-CoV-2 is a coronavirus responsible for the COVID-19 pandemic. Targeting the glycosylated Spike protein on the virus surface can prevent infections. Cyanovirin-N (CV-N), a lectin from cyanobacteria, can selectively target SARS-CoV-2 Spike glycans and inhibit viral infection in vitro and in vivo, showing potential as a broad-spectrum antiviral agent.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Pathology
Andres Santos, Madeline Sauer, Alexander J. Neil, Isaac H. Solomon, Jason L. Hornick, Drucilla J. Roberts, Bradley J. Quade, Carlos Parra-Herran
Summary: This study aimed to investigate the translation and accumulation of Spike protein in placental tissue after mRNA SARC-CoV-2 vaccination during pregnancy. The results showed that there was no significant accumulation of SARS-CoV-2 Spike protein in placental tissue after mRNA vaccination during pregnancy, supporting the safety of mRNA vaccines to the placental-fetal unit.
Article
Cell Biology
Lynda J. Partridge, Lucy Urwin, Martin J. H. Nicklin, David C. James, Luke R. Green, Peter N. Monk
Summary: The spike protein of SARS-CoV-2 binds primarily to ACE2 on target cells but may also involve other receptors. Heparin and glycosaminoglycans such as heparan sulfate and dermatan sulfate can inhibit the binding of spike protein to cells, indicating potential interactions with host cells beyond ACE2.
Article
Biology
Paul S. S. Kwon, Shirley Xu, Hanseul Oh, Seok-Joon Kwon, Andre L. Rodrigues, Maisha Feroz, Keith Fraser, Peng He, Fuming Zhang, Jung Joo Hong, Robert J. J. Linhardt, Jonathan S. S. Dordick
Summary: A polysulfated synthetic drug called suramin binds to the ACE2 receptor and heparan sulfate binding sites on SARS-CoV-2 receptor binding domains (RBDs), with preferential binding for the Omicron RBD and inhibition of infection by the Omicron variant in vitro. These findings suggest that suramin and other polysulfated molecules could be potential therapeutic and prophylactic options against COVID-19.
COMMUNICATIONS BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Hiam R. S. Arruda, Tulio M. Lima, Renata G. F. Alvim, Fernanda B. A. Victorio, Daniel P. B. Abreu, Federico F. Marsili, Karen D. Cruz, Mayra A. Marques, Patricia Sosa-Acosta, Mauricio Quinones-Vega, Jessica de S. Guedes, Fabio C. S. Nogueria, Jerson L. Silva, Leda R. Castilho, Guilherme A. P. de Oliveira
Summary: The severe acute respiratory syndrome caused a global pandemic. Mutations in the spike protein, an antigenic candidate for COVID-19 vaccines, have been observed in SARS-CoV-2. Comparative data of the ancestral and D614G spike, as well as other variants of concern, show that D614G has lower hydrophobic surface exposure and trimer stability, suggesting a temporary fitness advantage for virus spillover. The adaptation of SARS-CoV-2 also leads to decreased trimer stability and higher ACE-2 affinities in some variants, highlighting the importance of mapping the energetics and flexibility of these variants for vaccine development.
Article
Multidisciplinary Sciences
Qi Zhang, Weichun Tang, Eduardo Stancanelli, Eunkyung Jung, Zulfeqhar Syed, Vijayakanth Pagadala, Layla Saidi, Catherine Z. Chen, Peng Gao, Miao Xu, Ivan Pavlinov, Bing Li, Wenwei Huang, Liqiang Chen, Jian Liu, Hang Xie, Wei Zheng, Yihong Ye
Summary: Researchers found that SARS-CoV-2 infection causes fusion of infected cells with ACE2 positive neighboring cells through cell surface heparan sulfate, forming syncytia. Using chemical genetics and 4D confocal imaging, they identified heparan sulfate as a critical factor that stimulates spike-induced cell-cell fusion. Heparan sulfate binds to spike and promotes ACE2 clustering, facilitating fusion pore formation between ACE2-expressing and spike-transfected cells. Inhibition of heparan sulfate mitigates ACE2 clustering and syncytium formation.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Medicinal
Darya Stepanenko, Stephanie Budhan, Carlos Simmerling
Summary: In this application note, a tool is described that helps structural biologists in studying the SARS-CoV-2 spike glycoprotein. The tool fixes inconsistencies among deposited structures, calculates the distribution of requested distances between atoms, and provides a histogram and cumulative frequency of the calculated distribution.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Immunology
Kirill Kalnin, Timothy Plitnik, Michael Kishko, Jinrong Zhang, Donghui Zhang, Adrien Beauvais, Natalie G. Anosova, Tim Tibbitts, Josh DiNapoli, Gregory Ulinski, Peter Piepenhagen, Sheila M. Cummings, Dinesh S. Bangari, Susan Ryan, Po-Wei D. Huang, James Huleatt, Deanne Vincent, Katherine Fries, Shrirang Karve, Rebecca Goldman, Hardip Gopani, Anusha Dias, Khang Tran, Minnie Zacharia, Xiaobo Gu, Lianne Boeglin, Jonathan Abysalh, Jorel Vargas, Angela Beaulieu, Monic Shah, Travis Jeannotte, Kimberly Gillis, Sudha Chivukula, Ron Swearingen, Victoria Landolfi, Tong-Ming Fu, Frank DeRosa, Danilo Casimiro
Summary: Emergency use authorization of COVID vaccines has brought hope to mitigate the pandemic, but there is a need for additional effective vaccines. mRNA technologies offer an expedited alternative to traditional vaccine approaches, with the new mRNA vaccine candidate MRT5500 showing promising neutralizing antibody activity in animal models.
Article
Multidisciplinary Sciences
Dora Pinto, Maximilian M. Sauer, Nadine Czudnochowski, Jun Siong Low, M. Alejandra Tortorici, Michael P. Housley, Julia Noack, Alexandra C. Walls, John E. Bowen, Barbara Guarino, Laura E. Rosen, Julia di Iulio, Josipa Jerak, Hannah Kaiser, Saiful Islam, Stefano Jaconi, Nicole Sprugasci, Katja Culap, Rana Abdelnabi, Caroline Foo, Lotte Coelmont, Istvan Bartha, Siro Bianchi, Chiara Silacci-Fregni, Jessica Bassi, Roberta Marzi, Eneida Vetti, Antonino Cassotta, Alessandro Ceschi, Paolo Ferrari, Pietro E. Cippa, Olivier Giannini, Samuele Ceruti, Christian Garzoni, Agostino Riva, Fabio Benigni, Elisabetta Cameroni, Luca Piccoli, Matteo S. Pizzuto, Megan Smithey, David Hong, Amalio Telenti, Florian A. Lempp, Johan Neyts, Colin Havenar-Daughton, Antonio Lanzavecchia, Federica Sallusto, Gyorgy Snell, Herbert W. Virgin, Martina Beltramello, Davide Corti, David Veesler
Summary: The study identified five monoclonal antibodies from COVID-19 convalescent individuals that cross-react with multiple betacoronavirus spike glycoproteins, with one antibody (S2P6) showing broad neutralization of viruses from three different subgenera. This antibody reduced viral burden in hamsters challenged with SARS-CoV-2 by inhibiting membrane fusion, providing a framework for the design of pan-betacoronavirus vaccines for broad protection.
Article
Immunology
Danrong Shi, Tianhao Weng, Jie Wu, Chunyan Dai, Rui Luo, Keda Chen, Miaojin Zhu, Xiangyun Lu, Linfang Cheng, Qiuqiang Chen, Fumin Liu, Zhigang Wu, Haibo Wu, Changzhong Jin, Miao Guo, Zhe Chen, Nanping Wu, Hangping Yao, Min Zheng
Summary: The study found that antibodies produced after COVID-19 infection can remain detectable and effective for over a year, with different antibodies showing varied reactions over time.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Ramirez-Salinas Gema Lizbeth, Garcia-Machorro Jazmin, Correa-Basurto Jose, Martinez-Archundia Marlet
Summary: COVID-19, caused by a virus first identified in China in 2019, has spread to more than 216 countries. Pharmacological treatments based on similarities to the HIV virus have been proposed, as there is currently no vaccine. Research suggests that specific epitopes on the virus surface could be used in future vaccine design.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Chemistry, Physical
Kunal Dutta, Ammar D. Elmezayen, Anas Al-Obaidi, Wei Zhu, Olga Morozova, Sergey Shityakov, Ibrahim Khalifa
Summary: At the beginning of the new decade, the COVID-19 pandemic has severely affected modern human societies, but scientists have discovered three new antiviral peptides to combat SARS-CoV-2. These peptides can block the virus from binding to human cells, potentially serving as effective tools in fighting against the virus in the future.
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Article
Multidisciplinary Sciences
Sun Jin Kim, Zhong Yao, Morgan C. Marsh, Debra M. Eckert, Michael S. Kay, Anna Lyakisheva, Maria Pasic, Aiyush Bansal, Chaim Birnboim, Prabhat Jha, Yannick Galipeau, Marc-Andre Langlois, Julio C. Delgado, Marc G. Elgort, Robert A. Campbell, Elizabeth A. Middleton, Igor Stagljar, Shawn C. Owen
Summary: The authors report a surrogate virus neutralization assay called Neu-SATiN, which measures neutralization directly from sera and allows easy adaptation to variant-specific testing.
NATURE COMMUNICATIONS
(2022)
Correction
Chemistry, Physical
Ruichao Mao, Lihua Bie, Maofeng Xu, Xiaocong Wang, Jun Gao
Summary: This study focuses on antiviral drug design based on the opening mechanism of the spike glycoprotein in SARS-CoV-2.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Biotechnology & Applied Microbiology
Marco Rusnati, Giulia Paiardi, Chiara Tobia, Chiara Urbinati, Alessio Lodola, Pasqualina D'Ursi, Miriam Corrado, Riccardo Castelli, Rebecca C. Wade, Massimiliano Tognolini, Paola Chiodelli
Summary: UniPR1331, a derivative of 3 beta-hydroxy-Delta(5)-cholenic acid, has been shown to inhibit Eph-ephrin interaction and VEGFR2 activation, leading to the suppression of tumor cell-driven angiogenesis. These findings highlight the potential of Delta(5)-cholenic acid as a promising molecular scaffold for the development of multitarget antiangiogenic compounds.
CANCER GENE THERAPY
(2022)
Correction
Biotechnology & Applied Microbiology
Marco Rusnati, Giulia Paiardi, Chiara Tobia, Chiara Urbinati, Alessio Lodola, Pasqualina D'Ursi, Miriam Corrado, Riccardo Castelli, Rebecca C. Wade, Massimiliano Tognolini, Paola Chiodelli
CANCER GENE THERAPY
(2022)
Article
Microbiology
Philip Eisenberg, Leon Albert, Jonathan Teuffel, Eric Zitzow, Claudia Michaelis, Jane Jarick, Clemens Sehlke, Lisa Grosse, Nicole Bader, Ariane Nunes-Alves, Bernd Kreikemeyer, Hermann Schindelin, Rebecca C. Wade, Tomas Fiedler
Summary: The study reveals the importance of the non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase GapN in Streptococcus pyogenes and its potential as a target for antimicrobial substances that selectively kill S. pyogenes and other streptococci.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Thanasis Rogdakis, Despoina Charou, Alessia Latorrata, Eleni Papadimitriou, Alexandros Tsengenes, Christina Athanasiou, Marianna Papadopoulou, Constantina Chalikiopoulou, Theodora Katsila, Isbaal Ramos, Kyriakos C. Prousis, Rebecca C. Wade, Kyriaki Sidiropoulou, Theodora Calogeropoulou, Achille Gravanis, Ioannis Charalampopoulos
Summary: A new NGF mimetic, ENT-A013, has been identified to selectively activate TrkA receptor and exert neuroprotective effects, showing potential for therapeutic development against neurodegenerative disorders, such as Alzheimer's Disease.
Article
Chemistry, Medicinal
Ina Poehner, Antonio Quotadamo, Joanna Panecka-Hofman, Rosaria Luciani, Matteo Santucci, Pasquale Linciano, Giacomo Landi, Flavio Di Pisa, Lucia Dello Iacono, Cecilia Pozzi, Stefano Mangani, Sheraz Gul, Gesa Witt, Bernhard Ellinger, Maria Kuzikov, Nuno Santarem, Anabela Cordeiro-da-Silva, Maria P. Costi, Alberto Venturelli, Rebecca C. Wade
Summary: This study presents a systematic, multidisciplinary approach to the development of selective antiparasitic compounds with multiple targets. The approach combines computational fragment-based design and crystallographic structure determination to derive a structure-activity relationship for multitarget inhibition. The optimized compounds show promising inhibition against various parasitic targets while minimizing toxicity.
JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Siri C. van Keulen, Juliette Martin, Francesco Colizzi, Elisa Frezza, Daniel Trpevski, Nuria Cirauqui Diaz, Pietro Vidossich, Ursula Rothlisberger, Jeanette Hellgren Kotaleski, Rebecca C. Wade, Paolo Carloni
Summary: This study used simulation tools to uncover the molecular and subcellular mechanisms of AC function, with a focus on the AC5 isoform. The research revealed an inactive state of the enzyme in the presence of an inhibitory G alpha subunit, regardless of the presence of a stimulatory G alpha. The binding of G alpha subunits reshaped the free-energy landscape of the AC5 enzyme.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2023)
Review
Biology
Olivia Eriksson, Upinder Singh Bhalla, Kim T. Blackwell, Sharon M. Crook, Daniel Keller, Andrei Kramer, Marja-Leena Linne, Ausra Saudargiene, Rebecca C. Wade, Jeanette Hellgren Kotaleski
Summary: Modeling in neuroscience involves hypothesis-driven and data-driven approaches, with models constructed at different biological scales and levels of abstraction. However, a lack of interoperability, transparency, and reusability of models and workflows hinders the integration of models representing different scales and built using different methods. Applying the FAIR principles to models and workflows can facilitate integration and enhance understanding of the brain.
Article
Biotechnology & Applied Microbiology
Hanno Schmidt, Katharina Mauer, Manuel Glaser, Bahram Sayyaf Dezfuli, Soren Lukas Hellmann, Ana Lucia Silva Gomes, Falk Butter, Rebecca C. Wade, Thomas Hankeln, Holger Herlyn
Summary: This study presents a bioinformatics workflow for the identification of candidate target proteins in parasites. The workflow combines genomics, transcriptomics, and proteomics to reduce the time and cost in the development of new strategies against parasites. The results demonstrate the effectiveness of the workflow in identifying highly specific candidate targets in Acanthocephala (thorny-headed worms). Virtual ligand screening also identified promising compounds for the control of these parasites.
Review
Chemistry, Multidisciplinary
Abraham Muniz-Chicharro, Lane W. Votapka, Rommie E. Amaro, Rebecca C. Wade
Summary: Brownian dynamics (BD) is a computational method used to simulate molecular diffusion processes, and recent developments have improved its accuracy and expanded its applications. In biological research, BD is used to study the diffusive behavior of molecules under various conditions and to compute rate constants for molecular association and examine transport properties. The development of software packages for BD simulations has provided new features and expanded the range of questions that can be addressed.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2023)
Article
Chemistry, Physical
Ainara Claveras Cabezudo, Christina Athanasiou, Alexandros Tsengenes, Rebecca C. Wade
Summary: Reducing the nonbonded interactions between protein and water enables protein encapsulation in phospholipid micelles and bilayers.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Pharmacology & Pharmacy
Sergio Strizzi, Letizia Bernardo, Pasqualina D'Ursi, Chiara Urbinati, Andrea Bianco, Fiona Limanaqi, Andrea Manconi, Maria Milanesi, Alberto Macchi, Dario Di Silvestre, Adalberto Cavalleri, Giovanni Pareschi, Marco Rusnati, Mario Clerici, PierLuigi Mauri, Mara Biasin
Summary: A multidisciplinary approach was used to investigate the effect of UV-C irradiation on the S protein of SARS-CoV-2. The study identified the disruption of a disulphide bond, which resulted in a conformational change and reduced binding ability to the ACE2 receptor. The findings suggest the S2 domain of the S protein as a potential therapeutic target for preventing SARS-CoV-2 infection.
PHARMACOLOGICAL RESEARCH
(2023)