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Mallawarachchi S, Wang H, Mulgaonkar N, Irigoyen S, Padilla C, Mandadi K, Borneman J, Fernando S. Specifically targeting antimicrobial peptides for inhibition of Candidatus Liberibacter asiaticus. J Appl Microbiol 2024; 135:lxae061. [PMID: 38509024 DOI: 10.1093/jambio/lxae061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/21/2024] [Accepted: 03/19/2024] [Indexed: 03/22/2024]
Abstract
AIMS Huanglongbing (citrus greening) is a plant disease putatively caused by the unculturable Gram-negative bacterium Candidatus Liberibacter asiaticus (CLas), and it has caused severe damage to citrus plantations worldwide. There are no definitive treatments for this disease, and conventional disease control techniques have shown limited efficacy. This work presents an in silico evaluation of using specifically targeting anti-microbial peptides (STAMPs) consisting of a targeting segment and an antimicrobial segment to inhibit citrus greening by inhibiting the BamA protein of CLas, which is an outer membrane protein crucial for bacterial viability. METHODS AND RESULTS Initially, a set of peptides with a high affinity toward BamA protein were screened and evaluated via molecular docking and molecular dynamics simulations and were verified in vitro via bio-layer interferometry (BLI). In silico studies and BLI experiments indicated that two peptides, HASP2 and HASP3, showed stable binding to BamA. Protein structures for STAMPs were created by fusing known anti-microbial peptides (AMPs) with the selected short peptides. The binding of STAMPs to BamA was assessed using molecular docking and binding energy calculations. The attachment of high-affinity short peptides significantly reduced the free energy of binding for AMPs, suggesting that it would make it easier for the STAMPs to bind to BamA. Efficacy testing in vitro using a closely related CLas surrogate bacterium showed that STAMPs had greater inhibitory activity than AMP alone. CONCLUSIONS In silico and in vitro results indicate that the STAMPs can inhibit CLas surrogate Rhizobium grahamii more effectively compared to AMPs, suggesting that STAMPs can achieve better inhibition of CLas, potentially via enhancing the site specificity of AMPs.
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Affiliation(s)
- Samavath Mallawarachchi
- Department of Biological and Agricultural Engineering, Texas A&M University, College Station, TX 77843, United States
| | - Haoqi Wang
- Department of Biological and Agricultural Engineering, Texas A&M University, College Station, TX 77843, United States
| | - Nirmitee Mulgaonkar
- Department of Biological and Agricultural Engineering, Texas A&M University, College Station, TX 77843, United States
| | - Sonia Irigoyen
- Texas A&M AgriLife Research & Extension Center, Texas A&M University System, 2415 E Highway 83, Weslaco, TX 78596, United States
| | - Carmen Padilla
- Texas A&M AgriLife Research & Extension Center, Texas A&M University System, 2415 E Highway 83, Weslaco, TX 78596, United States
| | - Kranthi Mandadi
- Texas A&M AgriLife Research & Extension Center, Texas A&M University System, 2415 E Highway 83, Weslaco, TX 78596, United States
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, United States
- Institute for Advancing Health through Agriculture, Texas A&M AgriLife, College Station, TX 77843, United States
| | - James Borneman
- Department of Microbiology & Plant Pathology, University of California Riverside, Riverside, CA 92521, United States
| | - Sandun Fernando
- Department of Biological and Agricultural Engineering, Texas A&M University, College Station, TX 77843, United States
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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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Smith BL, Fernando S, King MD. Escherichia coli resistance mechanism AcrAB-TolC efflux pump interactions with commonly used antibiotics: a molecular dynamics study. Sci Rep 2024; 14:2742. [PMID: 38302495 PMCID: PMC10834472 DOI: 10.1038/s41598-024-52536-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 01/19/2024] [Indexed: 02/03/2024] Open
Abstract
While antibiotic resistance poses a threat from both Gram-positive bacteria (GPB) and Gram-negative bacteria (GNB), GNB pose a more imminent public health hazard globally. GNB are a threat to growing antibiotic resistance because of the complex makeup of the membrane. The AcrAB-TolC efflux pump is a known resistance mechanism of Escherichia coli (E. coli) cells. This study utilized molecular dynamics modeling to visualize some of the changes occurring at a molecular level when airborne bacteria are exposed to stress and antibiotics. This study was conducted to build upon previous experimental research showing that there is an increase in antibiotic resistance and efflux pump activity when exposed to aerosolization. AcrB and AcrAB-TolC proteins were simulated under standard and increased pressure to compare the effect of aerosolization on the binding to the three different antibiotics (puromycin (PUY), ampicillin (AMP) and sulfamethoxazole-trimethoprim (SXT)) to the AcrB binding site. Analysis such as root-mean-square deviation of atomic positions and root-mean-square fluctuation, the opening of TolC, and the significant molecular mechanics with generalized Born and surface area solvation (MM-GBSA) scores associated with specific ligands were recorded. Resistance in experimental data indicated a relationship between the docking scores and some ligand-protein interactions. Results showed that there was more flexibility in the proteins within simulations conducted under standard pressure for the AcrB protein and the full tripartite complex AcrAB-TolC, showing that increased pressure causes more rigidity. MM-GBSA scores, used to calculate the free energy of ligand-protein binding, did not show a significant change, but interestingly, the strongest MM-GBSA scores were for ligands that moved to another binding pocket and did not result in resistance or opening of the efflux pump. However, the ligand moved from the binding site and did not cause the opening of TolC to increase significantly, whereas PUY and AMP were bound to the binding site for the duration of all simulations. AMP ligands under increased pressure showed the largest change in opening of the TolC efflux pump and aligns with experimental data showing E. coli cells had the most resistance to AMP after aerosolization. These results, in addition to other real-time changes such as OM proteins and mutations of targets within the cell, could be used to delineate and mitigate antibiotic resistance mechanisms.
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Affiliation(s)
- Brooke L Smith
- Aerosol Technology Laboratory, Biological and Agricultural Engineering Department, Texas A&M University, College Station, TX, 77843, USA
| | - Sandun Fernando
- Aerosol Technology Laboratory, Biological and Agricultural Engineering Department, Texas A&M University, College Station, TX, 77843, USA
| | - Maria D King
- Aerosol Technology Laboratory, Biological and Agricultural Engineering Department, Texas A&M University, College Station, TX, 77843, USA.
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Zhang J, Gelain J, Schnabel G, Mallawarachchi S, Wang H, Mulgaonkar N, Karthikeyan R, Fernando S. Identification of Fungicide Combinations for Overcoming Plasmopara viticola and Botrytis cinerea Fungicide Resistance. Microorganisms 2023; 11:2966. [PMID: 38138109 PMCID: PMC10746041 DOI: 10.3390/microorganisms11122966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/21/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
Fungal diseases, including downy mildew (caused by Plasmopara viticola) and gray mold (caused by Botrytis cinerea), significantly impact the marketable yield of grapes produced worldwide. Cytochrome b of the mitochondrial respiratory chain of these two fungi is a key target for Quinone outside inhibitor (QoI)-based fungicide development. Since the mode of action (MOA) of QoI fungicides is restricted to a single site, the extensive usage of these fungicides has resulted in fungicide resistance. The use of fungicide combinations with multiple targets is an effective way to counter and slow down the development of fungicide resistance. Due to the high cost of in planta trials, in silico techniques can be used for the rapid screening of potential fungicides. In this study, a combination of in silico simulations that include Schrödinger Glide docking, molecular dynamics, and Molecular Mechanism-Generalized Born Surface Area calculation were used to screen the most potent QoI and non-QoI-based fungicide combinations to wild-type, G143A-mutated, F129L-mutated, and double-mutated versions that had both G143A and F129L mutations of fungal cytochrome b. In silico docking studies indicated that mandestrobin, famoxadone, captan, and thiram have a high affinity toward WT cytochrome b of Botrytis cinerea. Although the QoIs mandestrobin and famoxadone were effective for WT based on in vitro results, they were not broadly effective against G143A-mutated isolates. Famoxadone was only effective against one isolate with G143A-mutated cytochrome b. The non-QoI fungicides thiram and captan were effective against both WT and isolates with G143A-mutated cytochrome b. Follow-up in silico docking and molecular dynamics studies suggested that fungicide combinations consisting of famoxadone, mandestrobin, fenamidone, and thiram should be considered in field testing targeting Plasmopara viticola and Botrytis cinerea fungicide resistance.
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Affiliation(s)
- Junrui Zhang
- Department of Biological and Agricultural Engineering, Texas A&M University, College Station, TX 77845, USA
| | - Jhulia Gelain
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA
| | - Guido Schnabel
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA
| | - Samavath Mallawarachchi
- Department of Biological and Agricultural Engineering, Texas A&M University, College Station, TX 77845, USA
| | - Haoqi Wang
- Department of Biological and Agricultural Engineering, Texas A&M University, College Station, TX 77845, USA
| | - Nirmitee Mulgaonkar
- Department of Biological and Agricultural Engineering, Texas A&M University, College Station, TX 77845, USA
| | | | - Sandun Fernando
- Department of Biological and Agricultural Engineering, Texas A&M University, College Station, TX 77845, USA
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