In Silico Study of Bioactive Compounds from Yellow Bioherbal as Potential LpxC Protein Inhibitors for Controlling Pathogenic Bacteria in Broiler Chicken Intestinal
Bioherbal, a feed additive made from rhizome extract, exhibited promising capabilities in eradicating pathogenic bacteria residing within the digestive tracts of broiler chickens. The LpxC protein, a biosynthetic regulator of lipid A (a critical component of gram-negative bacterial cell walls), was...
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Fakultas Peternakan Universitas Brawijaya
2024-04-01
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| Series: | Jurnal Ilmu-Ilmu Peternakan |
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| Online Access: | https://jiip.ub.ac.id/index.php/jiip/article/view/2830 |
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| author | Zaen Yusuf Muhammad Halim Natsir Osfar Sjofjan |
| author_facet | Zaen Yusuf Muhammad Halim Natsir Osfar Sjofjan |
| author_sort | Zaen Yusuf |
| collection | DOAJ |
| description | Bioherbal, a feed additive made from rhizome extract, exhibited promising capabilities in eradicating pathogenic bacteria residing within the digestive tracts of broiler chickens. The LpxC protein, a biosynthetic regulator of lipid A (a critical component of gram-negative bacterial cell walls), was the focus of this research. Our primary objective was to assess the bioactive potential of bioherbal as a prospective inhibitor of UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine (LpxC) by employing in silico methods. Computational analyses were employed to scrutinize the interactions between the LpxC protein and various ligands on Bioherbal. Molecular docking served as the initial screening process, evaluating 48 bioactive compounds based on energy affinity, conformation values, and interactions with protein residues. The three compounds exhibiting the lowest binding affinities were subjected to molecular dynamics simulations. Molecular docking analysis revealed that most of the screened compounds exhibited low binding affinity for LpxC. Elephantorrhizol, zedoraldehyde, glechomanolide, demethoxycurcumin, curcumin, hexahydrocurcumin, gweicurculactone, germacrone, and 1,2-dihydrocurcumin exhibited lower binding affinities (<-7 kcal/mol). Elephantorrhizol, curcumin, and hexahydrocurcumin were selected for further analysis via molecular dynamics due to their similarity to native ligands. Molecular dynamics simulations revealed stable interactions of LpxC. In summary, these findings suggested that Bioherbal possesses the potential to function as an LpxC inhibitor, thereby offering a promising avenue for preventing the proliferation of gram-negative bacteria within the digestive tracts of broiler chickens. This computational study paves the way for further experimental investigations in this domain. |
| format | Article |
| id | doaj-art-2132accf3df04e6dba04be9b80dba664 |
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| issn | 0852-3681 2443-0765 |
| language | English |
| publishDate | 2024-04-01 |
| publisher | Fakultas Peternakan Universitas Brawijaya |
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| series | Jurnal Ilmu-Ilmu Peternakan |
| spelling | doaj-art-2132accf3df04e6dba04be9b80dba6642025-07-08T07:13:10ZengFakultas Peternakan Universitas BrawijayaJurnal Ilmu-Ilmu Peternakan0852-36812443-07652024-04-01341879810.21776/ub.jiip.2024.034.01.104259In Silico Study of Bioactive Compounds from Yellow Bioherbal as Potential LpxC Protein Inhibitors for Controlling Pathogenic Bacteria in Broiler Chicken IntestinalZaen Yusuf0Muhammad Halim Natsir1https://orcid.org/0000-0003-4830-7928Osfar Sjofjan2https://orcid.org/0000-0003-0115-3853Faculty of Animal Science, Brawijaya University, Jl. Veterans Malang 65145 East Java IndonesiaFaculty of Animal Science, Brawijaya University, Jl. Veterans Malang 65145 East Java IndonesiaFaculty of Animal Science, Brawijaya University, Jl. Veterans Malang 65145 East Java IndonesiaBioherbal, a feed additive made from rhizome extract, exhibited promising capabilities in eradicating pathogenic bacteria residing within the digestive tracts of broiler chickens. The LpxC protein, a biosynthetic regulator of lipid A (a critical component of gram-negative bacterial cell walls), was the focus of this research. Our primary objective was to assess the bioactive potential of bioherbal as a prospective inhibitor of UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine (LpxC) by employing in silico methods. Computational analyses were employed to scrutinize the interactions between the LpxC protein and various ligands on Bioherbal. Molecular docking served as the initial screening process, evaluating 48 bioactive compounds based on energy affinity, conformation values, and interactions with protein residues. The three compounds exhibiting the lowest binding affinities were subjected to molecular dynamics simulations. Molecular docking analysis revealed that most of the screened compounds exhibited low binding affinity for LpxC. Elephantorrhizol, zedoraldehyde, glechomanolide, demethoxycurcumin, curcumin, hexahydrocurcumin, gweicurculactone, germacrone, and 1,2-dihydrocurcumin exhibited lower binding affinities (<-7 kcal/mol). Elephantorrhizol, curcumin, and hexahydrocurcumin were selected for further analysis via molecular dynamics due to their similarity to native ligands. Molecular dynamics simulations revealed stable interactions of LpxC. In summary, these findings suggested that Bioherbal possesses the potential to function as an LpxC inhibitor, thereby offering a promising avenue for preventing the proliferation of gram-negative bacteria within the digestive tracts of broiler chickens. This computational study paves the way for further experimental investigations in this domain.https://jiip.ub.ac.id/index.php/jiip/article/view/2830bioherbalbroiler chickensintestinallpxcmolecular docking |
| spellingShingle | Zaen Yusuf Muhammad Halim Natsir Osfar Sjofjan In Silico Study of Bioactive Compounds from Yellow Bioherbal as Potential LpxC Protein Inhibitors for Controlling Pathogenic Bacteria in Broiler Chicken Intestinal Jurnal Ilmu-Ilmu Peternakan bioherbal broiler chickens intestinal lpxc molecular docking |
| title | In Silico Study of Bioactive Compounds from Yellow Bioherbal as Potential LpxC Protein Inhibitors for Controlling Pathogenic Bacteria in Broiler Chicken Intestinal |
| title_full | In Silico Study of Bioactive Compounds from Yellow Bioherbal as Potential LpxC Protein Inhibitors for Controlling Pathogenic Bacteria in Broiler Chicken Intestinal |
| title_fullStr | In Silico Study of Bioactive Compounds from Yellow Bioherbal as Potential LpxC Protein Inhibitors for Controlling Pathogenic Bacteria in Broiler Chicken Intestinal |
| title_full_unstemmed | In Silico Study of Bioactive Compounds from Yellow Bioherbal as Potential LpxC Protein Inhibitors for Controlling Pathogenic Bacteria in Broiler Chicken Intestinal |
| title_short | In Silico Study of Bioactive Compounds from Yellow Bioherbal as Potential LpxC Protein Inhibitors for Controlling Pathogenic Bacteria in Broiler Chicken Intestinal |
| title_sort | in silico study of bioactive compounds from yellow bioherbal as potential lpxc protein inhibitors for controlling pathogenic bacteria in broiler chicken intestinal |
| topic | bioherbal broiler chickens intestinal lpxc molecular docking |
| url | https://jiip.ub.ac.id/index.php/jiip/article/view/2830 |
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