1
|
Bosch A, Guzman HV, Pérez R. Adsorption-Driven Deformation and Footprints of the RBD Proteins in SARS-CoV-2 Variants on Biological and Inanimate Surfaces. J Chem Inf Model 2024; 64:5977-5990. [PMID: 39083670 PMCID: PMC11323246 DOI: 10.1021/acs.jcim.4c00460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 08/02/2024]
Abstract
Respiratory viruses, carried through airborne microdroplets, frequently adhere to surfaces, including plastics and metals. However, our understanding of the interactions between viruses and materials remains limited, particularly in scenarios involving polarizable surfaces. Here, we investigate the role of the receptor-binding domain (RBD) of the spike protein mutations on the adsorption of SARS-CoV-2 to hydrophobic and hydrophilic surfaces employing molecular simulations. To contextualize our findings, we contrast the interactions on inanimate surfaces with those on native biological interfaces, specifically the angiotensin-converting enzyme 2. Notably, we identify a 2-fold increase in structural deformations for the protein's receptor binding motif (RBM) onto inanimate surfaces, indicative of enhanced shock-absorbing mechanisms. Furthermore, the distribution of adsorbed amino acids (landing footprints) on the inanimate surface reveals a distinct regional asymmetry relative to the biological interface, with roughly half of the adsorbed amino acids arranged in opposite sites. In spite of the H-bonds formed at the hydrophilic substrate, the simulations consistently show a higher number of contacts and interfacial area with the hydrophobic surface, where the wild-type RBD adsorbs more strongly than the Delta or Omicron RBDs. In contrast, the adsorption of Delta and Omicron to hydrophilic surfaces was characterized by a distinctive hopping-pattern. The novel shock-absorbing mechanisms identified in the virus adsorption on inanimate surfaces show the embedded high-deformation capacity of the RBD without losing its secondary structure, which could lead to current experimental strategies in the design of virucidal surfaces.
Collapse
Affiliation(s)
- Antonio
M. Bosch
- Departamento
de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Horacio V. Guzman
- Departamento
de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Department
of Theoretical Physics, Jožef Stefan
Institute, SI-1000 Ljubljana, Slovenia
| | - Rubén Pérez
- Departamento
de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Condensed
Matter Physics Center (IFIMAC), Universidad
Autónoma de Madrid, E-28049 Madrid, Spain
| |
Collapse
|
2
|
Jin L, Mao Z. Living virus-based nanohybrids for biomedical applications. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2024; 16:e1923. [PMID: 37619605 DOI: 10.1002/wnan.1923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/26/2023]
Abstract
Living viruses characterized by distinctive biological functions including specific targeting, gene invasion, immune modulation, and so forth have been receiving intensive attention from researchers worldwide owing to their promising potential for producing numerous theranostic modalities against diverse pathological conditions. Nevertheless, concerns during applications, such as rapid immune clearance, altering immune activation modes, insufficient gene transduction efficiency, and so forth, highlight the crucial issues of excessive therapeutic doses and the associated biosafety risks. To address these concerns, synthetic nanomaterials featuring unique physical/chemical properties are frequently exploited as efficient drug delivery vehicles or treatments in biomedical domains. By constant endeavor, researchers nowadays can create adaptable living virus-based nanohybrids (LVN) that not only overcome the limitations of virotherapy, but also combine the benefits of natural substances and nanotechnology to produce novel and promising therapeutic and diagnostic agents. In this review, we discuss the fundamental physiochemical properties of the viruses, and briefly outline the basic construction methodologies of LVN. We then emphasize their distinct diagnostic and therapeutic performances for various diseases. Furthermore, we survey the foreseeable challenges and future perspectives in this interdisciplinary area to offer insights. This article is categorized under: Biology-Inspired Nanomaterials > Protein and Virus-Based Structures Therapeutic Approaches and Drug Discovery > Emerging Technologies.
Collapse
Affiliation(s)
- Lulu Jin
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China
| | - Zhengwei Mao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China
| |
Collapse
|
3
|
Zhang S, Wang N, Zhang Q, Guan R, Qu Z, Sun L, Li J. The Rise of Electroactive Materials in Face Masks for Preventing Virus Infections. ACS APPLIED MATERIALS & INTERFACES 2023; 15:48839-48854. [PMID: 37815875 DOI: 10.1021/acsami.3c10465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/12/2023]
Abstract
Air-transmitted pathogens may cause severe epidemics, posing considerable threats to public health and safety. Wearing a face mask is one of the most effective ways to prevent respiratory virus infection transmission. Especially since the new coronavirus pandemic, electroactive materials have received much attention in antiviral face masks due to their highly efficient antiviral capabilities, flexible structural design, excellent sustainability, and outstanding safety. This review first introduces the mechanism for preventing viral infection or the inactivation of viruses by electroactive materials. Then, the applications of electrostatic-, conductive-, triboelectric-, and microbattery-based materials in face masks are described in detail. Finally, the problems of various electroactive antiviral materials are summarized, and the prospects for their future development directions are discussed. In conclusion, electroactive materials have attracted great attention for antiviral face masks, and this review will provide a reference for materials scientists and engineers in antiviral materials and interfaces.
Collapse
Affiliation(s)
- Shaohua Zhang
- College of Textiles and Clothing, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, People's Republic of China
| | - Na Wang
- College of Textiles and Clothing, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, People's Republic of China
- Industrial Research Institute of Nonwovens and Technical Textiles, Shandong Center for Engineered Nonwovens, Qingdao 266071, People's Republic of China
| | - Qian Zhang
- Department of Respirology, Qingdao Women and Children's Hospital, Qingdao 266034, People's Republic of China
| | - Renzheng Guan
- College of Textiles and Clothing, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, People's Republic of China
| | - Zhenghai Qu
- College of Textiles and Clothing, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, People's Republic of China
| | - Lirong Sun
- College of Textiles and Clothing, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, People's Republic of China
| | - Jiwei Li
- College of Textiles and Clothing, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, People's Republic of China
- Industrial Research Institute of Nonwovens and Technical Textiles, Shandong Center for Engineered Nonwovens, Qingdao 266071, People's Republic of China
| |
Collapse
|
4
|
Addison-Smith I, Guzman HV, Cooper CD. Accurate Boundary Integral Formulations for the Calculation of Electrostatic Forces with an Implicit-Solvent Model. J Chem Theory Comput 2023; 19:2996-3006. [PMID: 37104704 DOI: 10.1021/acs.jctc.3c00021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
An accurate force calculation with the Poisson-Boltzmann equation is challenging, as it requires the electric field on the molecular surface. Here we present a calculation of the electric field on the solute-solvent interface that is exact for piecewise linear variations of the potential and analyze four different alternatives to compute the force using a boundary element method. We performed a verification exercise for two cases: the isolated and two interacting molecules. Our results suggest that the boundary element method outperforms the finite difference method, as the latter needs a much finer mesh than in solvation energy calculations to get acceptable accuracy in the force, whereas the same surface mesh as in a standard energy calculation is appropriate for the boundary element method. Among the four evaluated alternatives of force calculation, we saw that the most accurate one is based on the Maxwell stress tensor. However, for a realistic application, like the barnase-barstar complex, the approach based on variations of the energy functional, which is less accurate, gives equivalent results. This analysis is useful toward using the Poisson-Boltzmann equation for force calculations in applications where high accuracy is key, for example, to feed molecular dynamics models or to enable the study of the interaction between large molecular structures, like viruses adsorbed onto substrates.
Collapse
Affiliation(s)
- Ian Addison-Smith
- Department of Mechanical Engineering, Universidad Técnica Federico Santa María, 2390123 Valparaíso, Chile
| | - Horacio V Guzman
- Department of Theoretical Physics, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Christopher D Cooper
- Department of Mechanical Engineering, Universidad Técnica Federico Santa María, 2390123 Valparaíso, Chile
- Centro Científico Tecnológico de Valparaíso, Universidad Técnica Federico Santa María, 2390123 Valparaíso, Chile
| |
Collapse
|
5
|
Xu M, Ma R, Zhang C, Huang X, Gao X, Lv R, Chen X. Inactivation of Lactobacillus Bacteriophages by Dual Chemical Treatments. Pol J Microbiol 2023; 72:21-28. [PMID: 36929891 DOI: 10.33073/pjm-2023-004] [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: 10/10/2022] [Accepted: 01/02/2023] [Indexed: 03/18/2023] Open
Abstract
Phage contamination is one of the significant problems in the food fermentation industry, which eventually causes economic losses to the industry. Here, we investigated the viability of Lactobacillus plantarum phage P1 and P2 using various biocides treatments (ethanol, isopropanol, sodium hypochlorite and peracetic acid). Results indicated that phage P1 and P2 could be completely inactivated by treatment with 75% ethanol for 5 min, followed by 400 ppm of sodium hypochlorite treatment for 5 min. Phage P2 could be completely inactivated in the reverse sequence, while 800 ppm of sodium hypochlorite was required to achieve a similar effect for phage P1. Moreover, 100% isopropanol could increase the inactivating effect of 75% ethanol. This study may provide basic information on using multiple antimicrobials for phage control in laboratories and food plants.
Collapse
Affiliation(s)
- Ming Xu
- 1Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, P.R. China
- 2Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, P.R. China
- 3Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, Hohhot, P.R. China
| | - Ruirui Ma
- 1Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, P.R. China
- 2Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, P.R. China
- 3Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, Hohhot, P.R. China
| | - Can Zhang
- 1Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, P.R. China
- 2Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, P.R. China
- 3Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, Hohhot, P.R. China
| | - Xuecheng Huang
- 1Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, P.R. China
- 2Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, P.R. China
- 3Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, Hohhot, P.R. China
| | - Xin Gao
- 1Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, P.R. China
- 2Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, P.R. China
- 3Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, Hohhot, P.R. China
| | - Ruirui Lv
- 1Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, P.R. China
- 2Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, P.R. China
- 3Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, Hohhot, P.R. China
| | - Xia Chen
- 1Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, P.R. China
- 2Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, P.R. China
- 3Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, Hohhot, P.R. China
| |
Collapse
|