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Eigenfeld M, Lupp KFM, Schwaminger SP. Role of Natural Binding Proteins in Therapy and Diagnostics. Life (Basel) 2024; 14:630. [PMID: 38792650 PMCID: PMC11122601 DOI: 10.3390/life14050630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 05/02/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
This review systematically investigates the critical role of natural binding proteins (NBPs), encompassing DNA-, RNA-, carbohydrate-, fatty acid-, and chitin-binding proteins, in the realms of oncology and diagnostics. In an era where cancer continues to pose significant challenges to healthcare systems worldwide, the innovative exploration of NBPs offers a promising frontier for advancing both the diagnostic accuracy and therapeutic efficacy of cancer management strategies. This manuscript provides an in-depth examination of the unique mechanisms by which NBPs interact with specific molecular targets, highlighting their potential to revolutionize cancer diagnostics and therapy. Furthermore, it discusses the burgeoning research on aptamers, demonstrating their utility as 'nucleic acid antibodies' for targeted therapy and precision diagnostics. Despite the promising applications of NBPs and aptamers in enhancing early cancer detection and developing personalized treatment protocols, this review identifies a critical knowledge gap: the need for comprehensive studies to understand the diverse functionalities and therapeutic potentials of NBPs across different cancer types and diagnostic scenarios. By bridging this gap, this manuscript underscores the importance of NBPs and aptamers in paving the way for next-generation diagnostics and targeted cancer treatments.
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Affiliation(s)
- Marco Eigenfeld
- Otto-Loewi Research Center, Division of Medicinal Chemistry, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria
| | - Kilian F. M. Lupp
- Otto-Loewi Research Center, Division of Medicinal Chemistry, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria
| | - Sebastian P. Schwaminger
- Otto-Loewi Research Center, Division of Medicinal Chemistry, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
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Gossen KR, Zhang M, Nikolov ZL, Fernando SD, King MD. Binding behavior of receptor binding domain of the SARS-CoV-2 virus and ivermectin. Sci Rep 2024; 14:2743. [PMID: 38302638 PMCID: PMC10834942 DOI: 10.1038/s41598-024-53086-0] [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: 07/28/2023] [Accepted: 01/27/2024] [Indexed: 02/03/2024] Open
Abstract
The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), sparked an international debate on effective ways to prevent and treat the virus. Specifically, there were many varying opinions on the use of ivermectin (IVM) throughout the world, with minimal research to support either side. IVM is an FDA-approved antiparasitic drug that was discovered in the 1970s and was found to show antiviral activity. The objective of this study is to examine the binding behavior and rates of association and dissociation between SARS-CoV-2 receptor binding domain (RBD), IVM, and their combination using aminopropylsilane (APS) biosensors as surrogates for the hydrophobic interaction between the viral protein and human angiotensin-converting enzyme 2 (ACE2) receptors to determine the potential of IVM as a repurposed drug for SARS-CoV-2 prevention and treatment. The IVM, RBD, and combination binding kinetics were analyzed using biolayer interferometry (BLI) and validated with multiple in silico techniques including protein-ligand docking, molecular dynamics simulation, molecular mechanics-generalized Born surface area (MM-GBSA), and principal component analysis (PCA). Our results suggest that with increasing IVM concentrations the association rate with the hydrophobic biosensor increases with a simultaneous decrease in dissociation. Significant kinetic changes to RBD, when combined with IVM, were found only at a concentration a thousand times the approved dosage with minimal changes found over a 35-min time period. Our study suggests that IVM is not an effective preventative or treatment method at the currently approved dosage.
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Affiliation(s)
- Kasidy R Gossen
- Department of Biological and Agricultural Engineering, Texas A&M University, 2117 TAMU, College Station, TX, 77843, USA
| | - Meiyi Zhang
- Department of Biological and Agricultural Engineering, Texas A&M University, 2117 TAMU, College Station, TX, 77843, USA
| | - Zivko L Nikolov
- Department of Biological and Agricultural Engineering, Texas A&M University, 2117 TAMU, College Station, TX, 77843, USA
| | - Sandun D Fernando
- Department of Biological and Agricultural Engineering, Texas A&M University, 2117 TAMU, College Station, TX, 77843, USA
| | - Maria D King
- Department of Biological and Agricultural Engineering, Texas A&M University, 2117 TAMU, College Station, TX, 77843, USA.
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Zhang M, King MD. Temporal Variation of SARS-CoV-2 Levels in Wastewater from a Meat Processing Plant. Microorganisms 2023; 11:microorganisms11010174. [PMID: 36677465 PMCID: PMC9864470 DOI: 10.3390/microorganisms11010174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/04/2023] [Accepted: 01/07/2023] [Indexed: 01/12/2023] Open
Abstract
Wastewater-based surveillance (WBS) on SARS-CoV-2 has been proved to be an effective approach to estimate the prevalence of COVID-19 in communities and cities. However, its application was overlooked at smaller scale, such as a single facility. Meat processing plants are hotspots for COVID-19 outbreaks due to their unique environment that are favorable for the survival and persistence of SARS-CoV-2. This is the first known WBS study in meat processing plants. The goal was to understand the temporal variation of the SARS-CoV-2 levels in wastewater from a meat processing plant in Canada during a three-month campaign and to find any correlation with clinically confirmed cases in the surrounding city area. Higher SARS-CoV-2 concentrations and detection frequencies were observed in the solid fraction compared to the liquid fraction of the wastewater. The viruses can be preserved in the solid fraction of wastewater for up to 12 days. The wastewater virus level did not correlate to the city-wide COVID-19 cases due to the unmatching scales. WBS on SARS-CoV-2 in meat processing plants can be useful for identifying COVID-19 outbreaks in the facility and serve as an effective alternative when resources for routine individual testing are not available.
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Zareei S, Pourmand S, Amanlou M. Design of novel disturbing peptides against ACE2 SARS-CoV-2 spike-binding region by computational approaches. Front Pharmacol 2022; 13:996005. [PMID: 36438825 PMCID: PMC9692113 DOI: 10.3389/fphar.2022.996005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 10/24/2022] [Indexed: 10/12/2023] Open
Abstract
The SARS-CoV-2, the virus which is responsible for COVID-19 disease, employs its spike protein to recognize its receptor, angiotensin-converting enzyme 2 (ACE2), and subsequently enters the host cell. In this process, the receptor-binding domain (RBD) of the spike has an interface with the α1-helix of the peptidase domain (PD) of ACE2. This study focuses on the disruption of the protein-protein interaction (PPI) of RBD-ACE2. Among the residues in the template (which was extracted from the ACE2), those with unfavorable energies were selected for substitution by mutagenesis. As a result, a library of 140 peptide candidates was constructed and the binding affinity of each candidate was evaluated by molecular docking and molecular dynamics simulations against the α1-helix of ACE2. Finally, the most potent peptides P23 (GFNNYFPHQSYGFMPTNGVGY), P28 (GFNQYFPHQSYGFPPTNGVGY), and P31 (GFNRYFPHQSYGFCPTNGVGY) were selected and their dynamic behaviors were studied. The results showed peptide inhibitors increased the radius, surface accessible area, and overall mobility of residues of the protein. However, no significant alteration was seen in the key residues in the active site. Meanwhile, they can be proposed as promising agents against COVID-19 by suppressing the viral attachment and curbing the infection at its early stage. The designed peptides showed potency against beta, gamma, delta, and omicron variants of SARS-CoV-2.
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Affiliation(s)
- Sara Zareei
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Saeed Pourmand
- Department of Chemical Engineering, Faculty of Chemical and Petroleum Engineering, University of Tabriz, Tabriz, Iran
| | - Massoud Amanlou
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
- Experimental Medicine Research Center, Tehran University of Medical Sciences, Tehran, Iran
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Kalasariya HS, Patel NB, Gacem A, Alsufyani T, Reece LM, Yadav VK, Awwad NS, Ibrahium HA, Ahn Y, Yadav KK, Jeon BH. Marine Alga Ulva fasciata-Derived Molecules for the Potential Treatment of SARS-CoV-2: An In Silico Approach. Mar Drugs 2022; 20:md20090586. [PMID: 36135775 PMCID: PMC9506351 DOI: 10.3390/md20090586] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 12/13/2022] Open
Abstract
SARS-CoV-2 is the causative agent of the COVID-19 pandemic. This in silico study aimed to elucidate therapeutic efficacies against SARS-CoV-2 of phyco-compounds from the seaweed, Ulva fasciata. Twelve phyco-compounds were isolated and toxicity was analyzed by VEGA QSAR. Five compounds were found to be nonmutagenic, noncarcinogenic and nontoxic. Moreover, antiviral activity was evaluated by PASS. Binding affinities of five of these therapeutic compounds were predicted to possess probable biological activity. Fifteen SARS-CoV-2 target proteins were analyzed by the AutoDock Vina program for molecular docking binding energy analysis and the 6Y84 protein was determined to possess optimal binding affinities. The Desmond program from Schrödinger’s suite was used to study high performance molecular dynamic simulation properties for 3,7,11,15-Tetramethyl-2-hexadecen-1-ol—6Y84 for better drug evaluation. The ligand with 6Y84 had stronger binding affinities (−5.9 kcal/mol) over two standard drugs, Chloroquine (−5.6 kcal/mol) and Interferon α-2b (−3.8 kcal/mol). Swiss ADME calculated physicochemical/lipophilicity/water solubility/pharmacokinetic properties for 3,7,11,15-Tetramethyl-2-hexadecen-1-ol, showing that this therapeutic agent may be effective against SARS-CoV-2.
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Affiliation(s)
- Haresh S. Kalasariya
- Centre for Natural Products Discovery, School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK
| | - Nikunj B. Patel
- Microbiology Department, Sankalchand Patel University, Visnagar 384315, India
| | - Amel Gacem
- Department of Physics, Faculty of Sciences, University 20 Août 1955, Skikda 21000, Algeria
| | - Taghreed Alsufyani
- Department of Chemistry, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Lisa M. Reece
- Reece Life Science Consulting Agency, 819 N Amburn Rd, Texas City, TX 77591, USA
| | - Virendra Kumar Yadav
- Department of Biosciences, School of Liberal Arts & Sciences, Mody University of Science and Technology, Lakshmangarh, Sikar 332311, India
| | - Nasser S. Awwad
- Department of Chemistry, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Hala A. Ibrahium
- Biology Department, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
- Department of Semi Pilot Plant, Nuclear Materials Authority, El Maadi, P.O. Box 530, Cairo 11381, Egypt
| | - Yongtae Ahn
- Department of Earth Resources & Environmental Engineering, Hanyang University, 222-Wangsimni-ro, Seongdong-gu, Seoul 04763, Korea
| | - Krishna Kumar Yadav
- Faculty of Science and Technology, Madhyanchal Professional University, Ratibad, Bhopal 462044, India
- Correspondence: (K.K.Y.); (B.-H.J.)
| | - Byong-Hun Jeon
- Department of Earth Resources & Environmental Engineering, Hanyang University, 222-Wangsimni-ro, Seongdong-gu, Seoul 04763, Korea
- Correspondence: (K.K.Y.); (B.-H.J.)
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Baig TA, Zhang M, Smith BL, King MD. Environmental Effects on Viable Virus Transport and Resuspension in Ventilation Airflow. Viruses 2022; 14:616. [PMID: 35337023 PMCID: PMC8950092 DOI: 10.3390/v14030616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/12/2022] [Accepted: 03/14/2022] [Indexed: 01/27/2023] Open
Abstract
To understand how SARS-CoV-2 spreads indoors, in this study bovine coronavirus was aerosolized as simulant into a plexiglass chamber with coupons of metal, wood and plastic surfaces. After aerosolization, chamber and coupon surfaces were swiped to quantify the virus concentrations using quantitative polymerase chain reaction (qPCR). Bio-layer interferometry showed stronger virus association on plastic and metal surfaces, however, higher dissociation from wood in 80% relative humidity. Virus aerosols were collected with the 100 L/min wetted wall cyclone and the 50 L/min MD8 air sampler and quantitated by qPCR. To monitor the effect of the ventilation on the virus movement, PRD1 bacteriophages as virus simulants were disseminated in a ¾ scale air-conditioned hospital test room with twelve PM2.5 samplers at 15 L/min. Higher virus concentrations were detected above the patient's head and near the foot of the bed with the air inlet on the ceiling above, exhaust bottom left on the wall. Based on room layout, air measurements and bioaerosol collections computational flow models were created to visualize the movement of the virus in the room airflow. The addition of air curtain at the door minimized virus concentration while having the inlet and exhaust on the ceiling decreased overall aerosol concentration. Controlled laboratory experiments were conducted in a plexiglass chamber to gain more insight into the fundamental behavior of aerosolized SARS-CoV-2 and understand its fate and transport in the ambient environment of the hospital room.
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Affiliation(s)
| | | | | | - Maria D. King
- Aerosol Technology Laboratory, Biological & Agricultural Engineering Department, Texas A&M University, College Station, TX 77843, USA; (T.A.B.); (M.Z.); (B.L.S.)
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