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Vishweshwaraiah YL, Hnath B, Wang J, Chandler M, Mukherjee A, Yennawar NH, Booker SJ, Afonin KA, Dokholyan NV. A Piecewise Design Approach to Engineering a Miniature ACE2 Mimic to Bind SARS-CoV-2. ACS Appl Bio Mater 2024. [PMID: 38700999 DOI: 10.1021/acsabm.4c00222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
As the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues its global spread, the exploration of novel therapeutic and diagnostic strategies is still needed. The virus enters host cells by binding the angiotensin-converting enzyme 2 (ACE2) receptor through the spike protein. Here, we develop an engineered, small, stable, and catalytically inactive version of ACE2, termed miniature ACE2 (mACE2), designed to bind the spike protein with high affinity. Employing a magnetic nanoparticle-based assay, we harnessed the strong binding affinity of mACE2 to develop a sensitive and specific platform for the detection or neutralization of SARS-CoV-2. Our findings highlight the potential of engineered mACE2 as a valuable tool in the fight against SARS-CoV-2. The success of developing such a small reagent based on a piecewise molecular design serves as a proof-of-concept approach for the rapid deployment of such agents to diagnose and fight other viral diseases.
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Affiliation(s)
| | - Brianna Hnath
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania 17033-0850, United States
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania 16802, United States
| | - Jian Wang
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania 17033-0850, United States
| | - Morgan Chandler
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Arnab Mukherjee
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States
- The Howard Hughes Medical Institute, Penn State University, University Park, Pennsylvania 16802, United States
| | - Neela H Yennawar
- The Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802, United States
| | - Squire J Booker
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States
- The Howard Hughes Medical Institute, Penn State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry & Molecular Biology, Penn State University, University Park, Pennsylvania 16802, United States
| | - Kirill A Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Nikolay V Dokholyan
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania 17033-0850, United States
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania 16802, United States
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania 17033-0850, United States
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Padhi AK, Kalita P, Maurya S, Poluri KM, Tripathi T. From De Novo Design to Redesign: Harnessing Computational Protein Design for Understanding SARS-CoV-2 Molecular Mechanisms and Developing Therapeutics. J Phys Chem B 2023; 127:8717-8735. [PMID: 37815479 DOI: 10.1021/acs.jpcb.3c04542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
The continuous emergence of novel SARS-CoV-2 variants and subvariants serves as compelling evidence that COVID-19 is an ongoing concern. The swift, well-coordinated response to the pandemic highlights how technological advancements can accelerate the detection, monitoring, and treatment of the disease. Robust surveillance systems have been established to understand the clinical characteristics of new variants, although the unpredictable nature of these variants presents significant challenges. Some variants have shown resistance to current treatments, but innovative technologies like computational protein design (CPD) offer promising solutions and versatile therapeutics against SARS-CoV-2. Advances in computing power, coupled with open-source platforms like AlphaFold and RFdiffusion (employing deep neural network and diffusion generative models), among many others, have accelerated the design of protein therapeutics with precise structures and intended functions. CPD has played a pivotal role in developing peptide inhibitors, mini proteins, protein mimics, decoy receptors, nanobodies, monoclonal antibodies, identifying drug-resistance mutations, and even redesigning native SARS-CoV-2 proteins. Pending regulatory approval, these designed therapies hold the potential for a lasting impact on human health and sustainability. As SARS-CoV-2 continues to evolve, use of such technologies enables the ongoing development of alternative strategies, thus equipping us for the "New Normal".
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Affiliation(s)
- Aditya K Padhi
- Laboratory for Computational Biology & Biomolecular Design, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi 221005, Uttar Pradesh, India
| | - Parismita Kalita
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Shweata Maurya
- Laboratory for Computational Biology & Biomolecular Design, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi 221005, Uttar Pradesh, India
| | - Krishna Mohan Poluri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
- Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
- Department of Zoology, School of Life Sciences, North-Eastern Hill University, Shillong 793022, India
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Palma M. Epitopes and Mimotopes Identification Using Phage Display for Vaccine Development against Infectious Pathogens. Vaccines (Basel) 2023; 11:1176. [PMID: 37514992 PMCID: PMC10384025 DOI: 10.3390/vaccines11071176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/23/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Traditional vaccines use inactivated or weakened forms of pathogens which could have side effects and inadequate immune responses. To overcome these challenges, phage display has emerged as a valuable tool for identifying specific epitopes that could be used in vaccines. This review emphasizes the direct connection between epitope identification and vaccine development, filling a crucial gap in the field. This technique allows vaccines to be engineered to effectively stimulate the immune system by presenting carefully selected epitopes. Phage display involves screening libraries of random peptides or gene/genome fragments using serum samples from infected, convalescent, or vaccinated individuals. This method has been used to identify epitopes from various pathogens including SARS-CoV-2, Mycobacterium tuberculosis, hepatitis viruses, H5N1, HIV-1, Human T-lymphotropic virus 1, Plasmodium falciparum, Trypanosoma cruzi, and Dirofilaria repens. Bacteriophages offer advantages such as being immunogenic carriers, low production costs, and customization options, making them a promising alternative to traditional vaccines. The purpose of this study has been to highlight an approach that encompasses the entire process from epitope identification to vaccine production using a single technique, without requiring additional manipulation. Unlike conventional methods, phage display demonstrates exceptional efficiency and speed, which could provide significant advantages in critical scenarios such as pandemics.
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Affiliation(s)
- Marco Palma
- Institute for Globally Distributed Open Research and Education (IGDORE), 03181 Torrevieja, Spain
- Protheragen Inc., Ronkonkoma, NY 11779, USA
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Hartung J, McCann N, Doe E, Hayth H, Benkato K, Johnson MB, Viard M, Afonin KA, Khisamutdinov EF. Toehold-Mediated Shape Transition of Nucleic Acid Nanoparticles. ACS Appl Mater Interfaces 2023. [PMID: 37204867 DOI: 10.1021/acsami.3c01604] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
We introduce a toehold-mediated strand displacement strategy for regulated shape-switching of nucleic acid nanoparticles (NANPs) enabling their sequential transformation from triangular to hexagonal architectures at isothermal conditions. The successful shape transitions were confirmed by electrophoretic mobility shift assays, atomic force microscopy, and dynamic light scattering. Furthermore, implementation of split fluorogenic aptamers allowed for monitoring the individual transitions in real time. Three distinct RNA aptamers─malachite green (MG), broccoli, and mango─were embedded within NANPs as reporter domains to confirm shape transitions. While MG "lights up" within the square, pentagonal, and hexagonal constructs, the broccoli is activated only upon formation of pentagon and hexagon NANPs, and mango reports only the presence of hexagons. Moreover, the designed RNA fluorogenic platform can be employed to construct a logic gate that performs an AND operation with three single-stranded RNA inputs by implementing a non-sequential polygon transformation approach. Importantly, the polygonal scaffolds displayed promising potential as drug delivery agents and biosensors. All polygons exhibited effective cellular internalization followed by specific gene silencing when decorated with fluorophores and RNAi inducers. This work offers a new perspective for the design of toehold-mediated shape-switching nanodevices to activate different light-up aptamers for the development of biosensors, logic gates, and therapeutic devices in the nucleic acid nanotechnology.
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Affiliation(s)
- Jordan Hartung
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Nathan McCann
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Erwin Doe
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Hannah Hayth
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Kheiria Benkato
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - M Brittany Johnson
- Department of Biology, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Mathias Viard
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, United States
- Basic Science Program, Leidos Biomedical Research Inc. National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Kirill A Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Emil F Khisamutdinov
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
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Rolband L, Beasock D, Wang Y, Shu YG, Dinman JD, Schlick T, Zhou Y, Kieft JS, Chen SJ, Bussi G, Oukhaled A, Gao X, Šulc P, Binzel D, Bhullar AS, Liang C, Guo P, Afonin KA. Biomotors, viral assembly, and RNA nanobiotechnology: Current achievements and future directions. Comput Struct Biotechnol J 2022; 20:6120-37. [PMID: 36420155 DOI: 10.1016/j.csbj.2022.11.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 11/13/2022] Open
Abstract
The International Society of RNA Nanotechnology and Nanomedicine (ISRNN) serves to further the development of a wide variety of functional nucleic acids and other related nanotechnology platforms. To aid in the dissemination of the most recent advancements, a biennial discussion focused on biomotors, viral assembly, and RNA nanobiotechnology has been established where international experts in interdisciplinary fields such as structural biology, biophysical chemistry, nanotechnology, cell and cancer biology, and pharmacology share their latest accomplishments and future perspectives. The results summarized here highlight advancements in our understanding of viral biology and the structure-function relationship of frame-shifting elements in genomic viral RNA, improvements in the predictions of SHAPE analysis of 3D RNA structures, and the understanding of dynamic RNA structures through a variety of experimental and computational means. Additionally, recent advances in the drug delivery, vaccine design, nanopore technologies, biomotor and biomachine development, DNA packaging, RNA nanotechnology, and drug delivery are included in this critical review. We emphasize some of the novel accomplishments, major discussion topics, and present current challenges and perspectives of these emerging fields.
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