Identification of terpenoids as dihydropteroate synthase and dihydrofolate reductase inhibitors through structure-based virtual screening and molecular dynamic simulations
Bacterial infections are rising, and antimicrobial resistance (AMR) in bacteria has worsened the scenario, requiring extensive research to find alternative therapeutic agents. Terpenoids play an essential role in protecting plants from herbivores and pathogens. The present study was designed to focus on in silico evaluation of terpenoids for their affinity towards two necessary enzymes, i.e. DHFR and DHPS, which are involved in forming 5, 6, 7, 8-tetrahydrofolate, a key component in bacterial DNA synthesis proteins. Additionally, to account for activity against resistant bacteria, their affinity towards the L28R mutant of DHFR was also assessed in the study. The structure-based drug design approach was used to screen the compound library of terpenes for their interaction with active sites of DHFR and DHPS. Further, compounds were screened based on their dock score, pharmacokinetic properties, and binding affinities. A total of five compounds for each target protein were screened, having dock scores better than their respective standard drug molecules. CNP0169378 (-8.4 kcal/mol) and CNP0309455 (-6.5 kcal/mol) have been identified as molecules with a higher affinity toward the targets of DHFR and DHPS, respectively. At the same time, one molecule CNP0298407 (-5.8 kcal/mol for DHPS, -7.6 kcal/mol for DHFR, -6.1 kcal/mol for the L28R variant), has affinity for both proteins (6XG5 and 6XG4). All the molecules have good pharmacokinetic properties. We further validated the docking study by binding free energy calculations using the MM/GBSA approach and molecular dynamics simulations.Communicated by Ramaswamy H. Sarma.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2024 |
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| Erschienen: |
2024 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:42 |
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| Enthalten in: |
Journal of biomolecular structure & dynamics - 42(2024), 4 vom: 01. Feb., Seite 1966-1984 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Saini, Abhishek [VerfasserIn] |
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| Links: |
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| Anmerkungen: |
Date Completed 21.02.2024 Date Revised 21.02.2024 published: Print-Electronic Citation Status MEDLINE |
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| doi: |
10.1080/07391102.2023.2203249 |
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NLM356766241 |
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| 100 | 1 | |a Saini, Abhishek |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Identification of terpenoids as dihydropteroate synthase and dihydrofolate reductase inhibitors through structure-based virtual screening and molecular dynamic simulations |
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| 500 | |a Date Revised 21.02.2024 | ||
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| 520 | |a Bacterial infections are rising, and antimicrobial resistance (AMR) in bacteria has worsened the scenario, requiring extensive research to find alternative therapeutic agents. Terpenoids play an essential role in protecting plants from herbivores and pathogens. The present study was designed to focus on in silico evaluation of terpenoids for their affinity towards two necessary enzymes, i.e. DHFR and DHPS, which are involved in forming 5, 6, 7, 8-tetrahydrofolate, a key component in bacterial DNA synthesis proteins. Additionally, to account for activity against resistant bacteria, their affinity towards the L28R mutant of DHFR was also assessed in the study. The structure-based drug design approach was used to screen the compound library of terpenes for their interaction with active sites of DHFR and DHPS. Further, compounds were screened based on their dock score, pharmacokinetic properties, and binding affinities. A total of five compounds for each target protein were screened, having dock scores better than their respective standard drug molecules. CNP0169378 (-8.4 kcal/mol) and CNP0309455 (-6.5 kcal/mol) have been identified as molecules with a higher affinity toward the targets of DHFR and DHPS, respectively. At the same time, one molecule CNP0298407 (-5.8 kcal/mol for DHPS, -7.6 kcal/mol for DHFR, -6.1 kcal/mol for the L28R variant), has affinity for both proteins (6XG5 and 6XG4). All the molecules have good pharmacokinetic properties. We further validated the docking study by binding free energy calculations using the MM/GBSA approach and molecular dynamics simulations.Communicated by Ramaswamy H. Sarma | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Antibacterial agents | |
| 650 | 4 | |a DHFR | |
| 650 | 4 | |a DHPS | |
| 650 | 4 | |a molecular dynamics simulations | |
| 650 | 4 | |a terpenoids | |
| 650 | 4 | |a virtual screening | |
| 650 | 7 | |a Antimalarials |2 NLM | |
| 650 | 7 | |a Pyrimethamine |2 NLM | |
| 650 | 7 | |a Z3614QOX8W |2 NLM | |
| 650 | 7 | |a Folic Acid Antagonists |2 NLM | |
| 650 | 7 | |a Sulfadoxine |2 NLM | |
| 650 | 7 | |a 88463U4SM5 |2 NLM | |
| 650 | 7 | |a Dihydropteroate Synthase |2 NLM | |
| 650 | 7 | |a EC 2.5.1.15 |2 NLM | |
| 650 | 7 | |a Terpenes |2 NLM | |
| 650 | 7 | |a Tetrahydrofolate Dehydrogenase |2 NLM | |
| 650 | 7 | |a EC 1.5.1.3 |2 NLM | |
| 700 | 1 | |a Kumar, Amit |e verfasserin |4 aut | |
| 700 | 1 | |a Jangid, Kailash |e verfasserin |4 aut | |
| 700 | 1 | |a Kumar, Vinod |e verfasserin |4 aut | |
| 700 | 1 | |a Jaitak, Vikas |e verfasserin |4 aut | |
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