1
|
Zheng JJ, Li QZ, Wang Z, Wang X, Zhao Y, Gao X. Computer-aided nanodrug discovery: recent progress and future prospects. Chem Soc Rev 2024. [PMID: 39148378 DOI: 10.1039/d3cs00575e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Nanodrugs, which utilise nanomaterials in disease prevention and therapy, have attracted considerable interest since their initial conceptualisation in the 1990s. Substantial efforts have been made to develop nanodrugs for overcoming the limitations of conventional drugs, such as low targeting efficacy, high dosage and toxicity, and potential drug resistance. Despite the significant progress that has been made in nanodrug discovery, the precise design or screening of nanomaterials with desired biomedical functions prior to experimentation remains a significant challenge. This is particularly the case with regard to personalised precision nanodrugs, which require the simultaneous optimisation of the structures, compositions, and surface functionalities of nanodrugs. The development of powerful computer clusters and algorithms has made it possible to overcome this challenge through in silico methods, which provide a comprehensive understanding of the medical functions of nanodrugs in relation to their physicochemical properties. In addition, machine learning techniques have been widely employed in nanodrug research, significantly accelerating the understanding of bio-nano interactions and the development of nanodrugs. This review will present a summary of the computational advances in nanodrug discovery, focusing on the understanding of how the key interfacial interactions, namely, surface adsorption, supramolecular recognition, surface catalysis, and chemical conversion, affect the therapeutic efficacy of nanodrugs. Furthermore, this review will discuss the challenges and opportunities in computer-aided nanodrug discovery, with particular emphasis on the integrated "computation + machine learning + experimentation" strategy that can potentially accelerate the discovery of precision nanodrugs.
Collapse
Affiliation(s)
- Jia-Jia Zheng
- Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China.
| | - Qiao-Zhi Li
- Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China.
| | - Zhenzhen Wang
- Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China.
| | - Xiaoli Wang
- Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China.
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yuliang Zhao
- Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China.
| | - Xingfa Gao
- Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China.
| |
Collapse
|
2
|
Cárdenas-Moreno Y, González-Bacerio J, García Arellano H, Del Monte-Martínez A. Oxidoreductase enzymes: Characteristics, applications, and challenges as a biocatalyst. Biotechnol Appl Biochem 2023; 70:2108-2135. [PMID: 37753743 DOI: 10.1002/bab.2513] [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: 09/26/2022] [Accepted: 09/03/2023] [Indexed: 09/28/2023]
Abstract
Oxidoreductases are enzymes with distinctive characteristics that favor their use in different areas, such as agriculture, environmental management, medicine, and analytical chemistry. Among these enzymes, oxidases, dehydrogenases, peroxidases, and oxygenases are very interesting. Because their substrate diversity, they can be used in different biocatalytic processes by homogeneous and heterogeneous catalysis. Immobilization of these enzymes has favored their use in the solution of different biotechnological problems, with a notable increase in the study and optimization of this technology in the last years. In this review, the main structural and catalytical features of oxidoreductases, their substrate specificity, immobilization, and usage in biocatalytic processes, such as bioconversion, bioremediation, and biosensors obtainment, are presented.
Collapse
Affiliation(s)
- Yosberto Cárdenas-Moreno
- Laboratory for Enzyme Technology, Centre for Protein Studies, Faculty of Biology, University of Havana, Havana, Cuba
| | - Jorge González-Bacerio
- Laboratory for Enzyme Technology, Centre for Protein Studies, Faculty of Biology, University of Havana, Havana, Cuba
- Department of Biochemistry, Faculty of Biology, University of Havana, Havana, Cuba
| | - Humberto García Arellano
- Department of Environmental Sciences, Division of Health and Biological Sciences, Metropolitan Autonomous University, Lerma, Mexico, Mexico
| | - Alberto Del Monte-Martínez
- Laboratory for Enzyme Technology, Centre for Protein Studies, Faculty of Biology, University of Havana, Havana, Cuba
| |
Collapse
|
3
|
Huerta-Miranda GA, García-García WI, Vidal-Limon A, Miranda-Hernández M. Use of simplified models for theoretical prediction of the interactions between available antibodies and the receptor-binding domain of SARS-CoV-2 spike protein. J Biomol Struct Dyn 2023; 41:1018-1027. [PMID: 34935602 DOI: 10.1080/07391102.2021.2019123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The negative impact of infectious diseases like COVID-19 on public health and the global economy is evident. This pandemic represents a significant challenge for the scientific community to develop new practical analytical methods for accurately diagnosing emerging cases. Due to their selectivity and sensitivity, new methodologies based on antigen/antibody interactions to detect COVID-19 biomarkers are necessary. In this context, the theoretical, computational modeling reduces experimental efforts and saves resources for rational biosensor design. This study proposes using molecular dynamics to predict the interactions between the Receptor Binding Domain (RBD) of the SARS-CoV-2 spike protein simplified model and a set of highly characterized antibodies. The binding free energy of the antigen/antibody complexes was calculated for the simplified models and compared against the complete SARS-CoV-2 ectodomain to validate the methodology. The structural data derived from our molecular dynamics and end-point free energy calculations showed a positive correlation between both approximations, with a 0.82 Pearson correlation coefficient; t = 3.661, df = 3, p-value = 0.03522, with a 95% confident interval. Furthermore, we identified the interfacial residues that could generate covalent bonds with a specific chemical surface without perturbing the binding dynamics to develop highly sensitive and specific diagnostic devices. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- G A Huerta-Miranda
- Instituto de Energías Renovables, Universidad Nacional Autónoma de México, Temixco, Morelos, México
| | - W I García-García
- Instituto de Energías Renovables, Universidad Nacional Autónoma de México, Temixco, Morelos, México
| | - A Vidal-Limon
- Instituto de Energías Renovables, Universidad Nacional Autónoma de México, Temixco, Morelos, México
| | - M Miranda-Hernández
- Instituto de Energías Renovables, Universidad Nacional Autónoma de México, Temixco, Morelos, México
| |
Collapse
|
4
|
Tiwari S, Adupa V, Das DS, Anki Reddy K, Bharat TV. Structural and Dynamic Insights into SARS-CoV-2 Spike-Protein-Montmorillonite Interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:9186-9194. [PMID: 35855632 PMCID: PMC9344787 DOI: 10.1021/acs.langmuir.2c00837] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/21/2022] [Indexed: 06/01/2023]
Abstract
The spike (S) protein of SARS-CoV-2 has been found to play a decisive role in the cell entry mechanism of the virus and has been the prime target of most vaccine development efforts. Although numerous vaccines are already in use and more than half of the world population has been fully vaccinated, the emergence of new variants of the virus poses a challenge to the existing vaccines. Hence, developing an effective drug therapy is a crucial step in ending the pandemic. Nanoparticles can play a crucial role as a drug or a drug carrier and help tackle the pandemic effectively. Here, we performed explicit all-atom molecular dynamics simulations to probe interactions between S protein and Montmorillonite (MMT) nano clay surface. We built two systems with different counterions (Na+ and Ca2+), namely Na-MMT and Ca-MMT, to investigate the effect of different ions on S protein-MMT interaction. Structural modification of S protein was observed in the presence of MMT surface, particularly the loss of helical content of S protein. We revealed that electrostatic and hydrophobic interactions synergistically govern the S protein-MMT interactions. However, hydrophobic interactions were more pronounced in the Na-MMT system than in Ca-MMT. We also revealed residues and glycans of S protein closely interacting with the MMT surface. Interestingly, N165 and N343, which we found to be closely interacting with MMT in our simulations, also have a critical role in cell entry and in thwarting the cell's immune response in recent studies. Overall, our work provides atomistic insights into S protein-MMT interaction and enriches our understanding of the nanoparticle-S protein interaction mechanism, which will help develop advanced therapeutic techniques in the future.
Collapse
Affiliation(s)
- Shivam Tiwari
- Department
of Chemical Engineering, Indian Institute
of Technology, Guwahati, Assam 781039, India
| | - Vasista Adupa
- Department
of Chemical Engineering, Indian Institute
of Technology, Guwahati, Assam 781039, India
| | - Dhanesh Sing Das
- Department
of Civil Engineering, Indian Institute of
Technology, Guwahati, Assam 781039, India
| | - K. Anki Reddy
- Department
of Chemical Engineering, Indian Institute
of Technology, Tirupati, Andhra Pradesh 517506, India
| | | |
Collapse
|
5
|
Gold Nanoparticle-Mediated Lateral Flow Assays for Detection of Host Antibodies and COVID-19 Proteins. NANOMATERIALS 2022; 12:nano12091456. [PMID: 35564165 PMCID: PMC9102158 DOI: 10.3390/nano12091456] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/17/2022] [Accepted: 04/19/2022] [Indexed: 01/15/2023]
Abstract
Coronaviruses, that are now well-known to the public, include a family of viruses that can cause severe acute respiratory syndrome (SARS) and other respiratory diseases, such as Middle East respiratory syndrome (MERS). Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the seventh member of this coronavirus family, was detected in 2019 and can cause a number of respiratory symptoms, from dry cough and fever to fatal viral pneumonia. Various diagnostic assays ranging from real-time polymerase chain reaction (RT-PCR) to point-of-care medical diagnostic systems have been developed for detection of viral components or antibodies targeting the virus. Point-of-care assays allow rapid diagnostic assessment of infectious patients. Such assays are ideally simple, low-cost, portable tests with the possibility for on-site field detection that do not require skilled staff, sophisticated equipment, or sample pretreatment, as compared to RT-PCR. Since early 2021 when new SARS-CoV-2 variants of concern increased, rapid tests became more crucial in the disease management cycle. Among rapid tests, gold nanoparticle (GNP)-based lateral flow assays (LFAs) have high capacity for performing at the bedside, paving the way to easy access to diagnosis results. In this review, GNP-based LFAs used for either COVID-19 proteins or human response antibodies are summarized and recommendations for their improvement have been suggested.
Collapse
|
6
|
Džupponová V, Žoldák G. Salt-dependent passive adsorption of IgG1κ-type monoclonal antibodies on hydrophobic microparticles. Biophys Chem 2021; 275:106609. [PMID: 33975078 DOI: 10.1016/j.bpc.2021.106609] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/27/2021] [Accepted: 04/29/2021] [Indexed: 11/27/2022]
Abstract
Understanding how antibodies adsorb on solid surfaces is essential for developing effective approaches to control this process. In this study, passive adsorptions on the hydrophobic solid surface of a polystyrene microparticle (MP) of two highly similar IgG1 κ-type monoclonal antibodies (mAbs), rituximab, and trastuzumab, were examined in the presence of Hofmeister salts. Except of kosmotropic salts, the screening of electrostatic interactions using salts reduces the passive adsorption of mAbs on MP. To better understand the ion-specific adsorption process, salt-dependent Langmuir isotherm parameters were obtained and correlated for two mAbs. We find that while their maximum adsorption capacities to MPs are highly correlated (r > 0.9), the salt-dependent profiles of adsorption binding constants, Kobs, differ substantially. For rituximab, Kobs increases >10-fold in an ion-specific manner; for trastuzumab, Kobs remains constant. We conclude that even minor sequence variations among the mAbs can affect the adsorption, as well as the molecular forces attracting proteins to a solid surface. This difference might originate from the heterogeneous orientation of the adsorbed mAbs.
Collapse
Affiliation(s)
- Veronika Džupponová
- Department of Biophysics, Faculty of Science, P. J. Šafárik University, Jesenna 5, 040 01 Košice, Slovakia
| | - Gabriel Žoldák
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, P.J. Šafárik University, Trieda SNP 1, 040 11 Košice, Slovakia.
| |
Collapse
|
7
|
Farouq MA, Al Qaraghuli MM, Kubiak-Ossowska K, Ferro VA, Mulheran PA. Biomolecular interactions with nanoparticles: applications for coronavirus disease 2019. Curr Opin Colloid Interface Sci 2021; 54:101461. [PMID: 33907504 PMCID: PMC8062422 DOI: 10.1016/j.cocis.2021.101461] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nanoparticles are small particles sized 1-100 nm, which have a large surface-to-volume ratio, allowing efficient adsorption of drugs, proteins, and other chemical compounds. Consequently, functionalized nanoparticles have potential diagnostic and therapeutic applications. A variety of nanoparticles have been studied, including those constructed from inorganic materials, biopolymers, and lipids. In this review, we focus on recent work targeting the severe acute respiratory syndrome coronavirus 2 virus that causes coronavirus disease (COVID-19). Understanding the interactions between coronavirus-specific proteins (such as the spike protein and its host cell receptor angiotensin-converting enzyme 2) with different nanoparticles paves the way to the development of new therapeutics and diagnostics that are urgently needed for the fight against COVID-19, and indeed for related future viral threats that may emerge.
Collapse
Affiliation(s)
- Mohammed A.H. Farouq
- Department of Chemical and Process Engineering, University of Strathclyde, 75 Montrose Street, Glasgow, G1 1XJ, UK,Corresponding author: Farouq, M.A.H
| | - Mohammed M. Al Qaraghuli
- Department of Chemical and Process Engineering, University of Strathclyde, 75 Montrose Street, Glasgow, G1 1XJ, UK
| | - Karina Kubiak-Ossowska
- Department of Physics/Archie-West HPC, University of Strathclyde, 107 Rottenrow East, Glasgow, G4 0NG, UK
| | - Valerie A. Ferro
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | - Paul A. Mulheran
- Department of Chemical and Process Engineering, University of Strathclyde, 75 Montrose Street, Glasgow, G1 1XJ, UK
| |
Collapse
|
8
|
Das Mukhopadhyay C, Sharma P, Sinha K, Rajarshi K. Recent trends in analytical and digital techniques for the detection of the SARS-Cov-2. Biophys Chem 2021; 270:106538. [PMID: 33418105 PMCID: PMC7768211 DOI: 10.1016/j.bpc.2020.106538] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/30/2020] [Accepted: 12/24/2020] [Indexed: 12/26/2022]
Abstract
The current global outbreak of COVID-19 due to SARS-CoV-2 is an unprecedented humanitarian crisis. Considering the gravity of its impact there is an immediate need to develop a detection technique that is sensitive, specific, fast, and affordable for the clinical diagnosis of the disease. Real time Polymerase Chain Reaction (RT-PCR)-based detection platforms are contemplated to be the gold standard to detect viral RNA. However, that may be susceptible to errors, and there is a risk of obtaining false results, which ultimately compromises the strategy of efficient disease management. Several modern techniques exhibiting assured results with enhanced sensitivity and specificity against the SARS-CoV-2 associated viral components or immune response against it have been developed and may be implemented. The review deals with the conventional RT-PCR detection techniques and compares them to other detection platforms viz., biosensor based detection of antigens, fluorescent or colorimetric detection systems including CRISPR-Cas 13 based SHERLOCK kit, CRISPR Cas-9 based FELUDA test kit, CRISPR DETECTR kit, Next Generation Sequencing or microarray-based kits. These modern techniques are great as a point of care detection methods but should be followed by RT PCR based detection for the confirmation of COVID-19 status.
Collapse
Affiliation(s)
- Chitrangada Das Mukhopadhyay
- Centre for Healthcare Science and Technology, Indian Institute of Engineering Science and Technology (IIEST), Shibpur, Howrah, West Bengal 711103, India.
| | - Pramita Sharma
- Centre for Healthcare Science and Technology, Indian Institute of Engineering Science and Technology (IIEST), Shibpur, Howrah, West Bengal 711103, India
| | - Koel Sinha
- Centre for Healthcare Science and Technology, Indian Institute of Engineering Science and Technology (IIEST), Shibpur, Howrah, West Bengal 711103, India
| | - Keshav Rajarshi
- School of Community Science and Technology, Indian Institute of Engineering Science and Technology (IIEST), Shibpur, Howrah, West Bengal 711103, India
| |
Collapse
|
9
|
Watase Y, Takahashi H, Ushio K, Fujii M, Sakai M. IR super-resolution imaging of avian feather keratins detected by using vibrational sum-frequency generation. Biophys Chem 2020; 267:106482. [PMID: 33022568 DOI: 10.1016/j.bpc.2020.106482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/19/2020] [Accepted: 09/19/2020] [Indexed: 11/19/2022]
Abstract
IR super-resolution imaging of the cross section of the rachis of an avian feather was carried out by using a vibrational sum-frequency generation (VSFG) detected IR microscope with a sub-micrometer spatial resolution. In the YYX polarization combination, we clearly observed strong signals in the entire region of the rachis at the amide I vibration of β-keratin. On the other hand, the signal disappears from most of the cross section in the XXY polarization combination. Because the VSFG imaging detects the signal only from the interface, we conclude that the interfacial deflection inside of a rachis was detected.
Collapse
Affiliation(s)
- Yukihisa Watase
- Laboratory for Chemistry and Life Science, Tokyo Institute of Technology 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Hirona Takahashi
- Department of Chemistry, Faculty of Science, Okayama University of Science 1-1 Ridai-cho, Kita-ku, Okayama 700-0005, Japan
| | - Kohei Ushio
- Laboratory for Chemistry and Life Science, Tokyo Institute of Technology 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science, Tokyo Institute of Technology 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan.
| | - Makoto Sakai
- Department of Chemistry, Faculty of Science, Okayama University of Science 1-1 Ridai-cho, Kita-ku, Okayama 700-0005, Japan.
| |
Collapse
|
10
|
Rui L, Haonan L, Wanyi C. Silico analysis of interaction between full-length SARS-CoV2 S protein with human Ace2 receptor: Modelling, docking, MD simulation. Biophys Chem 2020; 267:106472. [PMID: 32916377 PMCID: PMC7468316 DOI: 10.1016/j.bpc.2020.106472] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/19/2020] [Accepted: 08/27/2020] [Indexed: 12/14/2022]
Abstract
Many key residues, which mediate the interaction between SARS-CoV2 spike glycoprotein (S protein) and human ACE2 receptor, have been reviewed using the SARS-CoV2 S spike protein with human ACE2 complex. The initial SARS-CoV2 S protein and ACE2 protein complex structure is formed by RBD structure of SARS-CoV2 S protein and ACE2 protein. However, the cryo-EM structure study targeting SARS-Cov S protein with human ACE2 complex has shown that there exist different binding conformations during the binding process facing ACE2 protein. It suggests the interaction between SARS-CoV2 S spike protein complex might have different binding conformations, which request full-length of SARS-CoV2 S protein complex in the structure-functional analysis. In this study, we built a full-length SARS-CoV2 S protein with human ACE2 complex by computational methods. Residues K31, H34, E35 in ACE2 protein were showed both in our full-length model and RBD structure model, which recognized as critical residues in previous studies. Surprisingly, ACE2 residues E564, R559, N556 were only found participating in the interaction of our full-length model, which suggested the full-length model has bigger binding interface. This finding was further supported by the interaction network of full-length model and RBD model. Meanwhile, the method bias was taken into consideration. Eventually, the MM-PBSA results showed the full-length model had a stronger binding free energy (almost 5-fold) than the RBD structure model of SARS-CoV2 S spike protein complex. In computational level, we present a stronger binding model containing a full-length structure of SARS-CoV2 S protein with ACE2 complex. In this study, we built a full-length SARS-Cov-2 S protein with human ACE2 complex by computational methods, which might present the bigger binding info. Residues K31, H34, E35 in ACE2 protein were showed as critical residues in previous studies in our full-length model and RBD structure model. ACE2 residues E564, R559, N556 were found in the interaction of our full-length model. The full-length model had a stronger binding free energy (almost 5-fold) than the RBD structure model. In computational level, we present a stronger binding model containing a full-length structure of SARS-CoV-2 S protein with ACE2 complex.
Collapse
Affiliation(s)
- Li Rui
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
| | - Li Haonan
- Key Laboratory of Tropical Biological Resources, Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Chen Wanyi
- Key Laboratory of Tropical Biological Resources, Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| |
Collapse
|