In-silico studies to recognize repurposing therapeutics toward arginase-I inhibitors as a potential onco-immunomodulators
Rudolf Virchow was the first person to point out the important link between immune function and cancer. He did this by noticing that leukocytes were often found in tumors. Overexpression of arginase 1 (ARG1) and inducible nitric oxide synthase (iNOS) in myeloid-derived suppressor cells (MDSCs) and t...
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2023-04-01
|
| Series: | Frontiers in Pharmacology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fphar.2023.1129997/full |
| _version_ | 1797844973807206400 |
|---|---|
| author | Magdi E. A. Zaki Sami A. Al-Hussain Aamal A. Al-Mutairi Abdul Samad Arabinda Ghosh Somdatta Chaudhari Pravin N. Khatale Prashant Ajmire Rahul D. Jawarkar |
| author_facet | Magdi E. A. Zaki Sami A. Al-Hussain Aamal A. Al-Mutairi Abdul Samad Arabinda Ghosh Somdatta Chaudhari Pravin N. Khatale Prashant Ajmire Rahul D. Jawarkar |
| author_sort | Magdi E. A. Zaki |
| collection | DOAJ |
| description | Rudolf Virchow was the first person to point out the important link between immune function and cancer. He did this by noticing that leukocytes were often found in tumors. Overexpression of arginase 1 (ARG1) and inducible nitric oxide synthase (iNOS) in myeloid-derived suppressor cells (MDSCs) and tumour-associated macrophages (TAMs) depletes both intracellular and extracellular arginine. TCR signalling is slowed as a result, and the same types of cells produce reactive oxygen and nitrogen species (ROS and RNS), which aggravates the situation. Human arginase I is a double-stranded manganese metalloenzyme that helps L-arginine break down into L-ornithine and urea. Thus, a quantitative structure-activity relationship (QSAR) analysis was performed to unearth the unrecognised structural aspects crucial for arginase-I inhibition. In this work, a balanced QSAR model with good prediction performance and clear mechanistic interpretation was developed using a dataset of 149 molecules encompassing a broad range of structural scaffolds and compositions. The model was made to meet OECD standards, and all of its validation parameters have values that are higher than the minimum requirements (R2tr = 0.89, Q2LMO = 0.86, and R2ex = 0.85). The present QSAR study linked structural factors to arginase-I inhibitory action, including the proximity of lipophilic atoms to the molecule’s centre of mass (within 3A), the position of the donor to the ring nitrogen (exactly 3 bonds away), and the surface area ratio. As OAT-1746 and two others are the only arginase-I inhibitors in development at the time, we have performed a QSAR-based virtual screening with 1650 FDA compounds taken from the zinc database. In this screening, 112 potential hit compounds were found to have a PIC50 value of less than 10 nm against the arginase-I receptor. The created QSAR model’s application domain was evaluated in relation to the most active hit molecules identified using QSAR-based virtual screening, utilising a training set of 149 compounds and a prediction set of 112 hit molecules. As shown in the Williams plot, the top hit molecule, ZINC000252286875, has a low leverage value of HAT i/i h* = 0.140, placing it towards the boundary of the usable range. Furthermore, one of 112 hit molecules with a docking score of −10.891 kcal/mol (PIC50 = 10.023 M) was isolated from a study of arginase-I using molecular docking. Protonated ZINC000252286875-linked arginase-1 showed 2.9 RMSD, whereas non-protonated had 1.8. RMSD plots illustrate protein stability in protonated and non-protonated ZINC000252286875-bound states. Protonated-ZINC000252286875-bound proteins contain 25 Rg. The non-protonated protein-ligand combination exhibits a 25.2-Rg, indicating compactness. Protonated and non-protonated ZINC000252286875 stabilised protein targets in binding cavities posthumously. Significant root mean square fluctuations (RMSF) were seen in the arginase-1 protein at a small number of residues for a time function of 500 ns in both the protonated and unprotonated states. Protonated and non-protonated ligands interacted with proteins throughout the simulation. ZINC000252286875 bound Lys64, Asp124, Ala171, Arg222, Asp232, and Gly250. Aspartic acid residue 232 exhibited 200% ionic contact. 500-ns simulations-maintained ions. Salt bridges for ZINC000252286875 aided docking. ZINC000252286875 created six ionic bonds with Lys68, Asp117, His126, Ala171, Lys224, and Asp232 residues. Asp117, His126, and Lys224 showed 200% ionic interactions. In protonated and deprotonated states, GbindvdW, GbindLipo, and GbindCoulomb energies played crucial role. Moreover, ZINC000252286875 meets all of the ADMET standards to serve as a drug. As a result, the current analyses were successful in locating a novel and potent hit molecule that inhibits arginase-I effectively at nanomolar concentrations. The results of this investigation can be used to develop brand-new arginase I inhibitors as an alternative immune-modulating cancer therapy. |
| first_indexed | 2024-04-09T17:31:02Z |
| format | Article |
| id | doaj.art-0dbc6cc9656a43e2abb9d584f7e1244a |
| institution | Directory Open Access Journal |
| issn | 1663-9812 |
| language | English |
| last_indexed | 2024-04-09T17:31:02Z |
| publishDate | 2023-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Pharmacology |
| spelling | doaj.art-0dbc6cc9656a43e2abb9d584f7e1244a2023-04-18T04:16:19ZengFrontiers Media S.A.Frontiers in Pharmacology1663-98122023-04-011410.3389/fphar.2023.11299971129997In-silico studies to recognize repurposing therapeutics toward arginase-I inhibitors as a potential onco-immunomodulatorsMagdi E. A. Zaki0Sami A. Al-Hussain1Aamal A. Al-Mutairi2Abdul Samad3Arabinda Ghosh4Somdatta Chaudhari5Pravin N. Khatale6Prashant Ajmire7Rahul D. Jawarkar8Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi ArabiaDepartment of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi ArabiaDepartment of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi ArabiaDepartment of Pharmaceutical Chemistry, Faculty of Pharmacy, Tishk International University, Erbil, Kurdistan Region, IraqMicrobiology Division, Department of Botany, Gauhati University, Guwahati, IndiaDepartment of Pharmaceutical Chemistry, Progressive Education Society’s Modern College of Pharmacy, Pune, IndiaDepartment of Medicinal Chemistry, Dr Rajendra Gode Institute of Pharmacy, Amravati, Maharashtra, IndiaDepartment of Medicinal Chemistry, Dr Rajendra Gode Institute of Pharmacy, Amravati, Maharashtra, IndiaDepartment of Medicinal Chemistry, Dr Rajendra Gode Institute of Pharmacy, Amravati, Maharashtra, IndiaRudolf Virchow was the first person to point out the important link between immune function and cancer. He did this by noticing that leukocytes were often found in tumors. Overexpression of arginase 1 (ARG1) and inducible nitric oxide synthase (iNOS) in myeloid-derived suppressor cells (MDSCs) and tumour-associated macrophages (TAMs) depletes both intracellular and extracellular arginine. TCR signalling is slowed as a result, and the same types of cells produce reactive oxygen and nitrogen species (ROS and RNS), which aggravates the situation. Human arginase I is a double-stranded manganese metalloenzyme that helps L-arginine break down into L-ornithine and urea. Thus, a quantitative structure-activity relationship (QSAR) analysis was performed to unearth the unrecognised structural aspects crucial for arginase-I inhibition. In this work, a balanced QSAR model with good prediction performance and clear mechanistic interpretation was developed using a dataset of 149 molecules encompassing a broad range of structural scaffolds and compositions. The model was made to meet OECD standards, and all of its validation parameters have values that are higher than the minimum requirements (R2tr = 0.89, Q2LMO = 0.86, and R2ex = 0.85). The present QSAR study linked structural factors to arginase-I inhibitory action, including the proximity of lipophilic atoms to the molecule’s centre of mass (within 3A), the position of the donor to the ring nitrogen (exactly 3 bonds away), and the surface area ratio. As OAT-1746 and two others are the only arginase-I inhibitors in development at the time, we have performed a QSAR-based virtual screening with 1650 FDA compounds taken from the zinc database. In this screening, 112 potential hit compounds were found to have a PIC50 value of less than 10 nm against the arginase-I receptor. The created QSAR model’s application domain was evaluated in relation to the most active hit molecules identified using QSAR-based virtual screening, utilising a training set of 149 compounds and a prediction set of 112 hit molecules. As shown in the Williams plot, the top hit molecule, ZINC000252286875, has a low leverage value of HAT i/i h* = 0.140, placing it towards the boundary of the usable range. Furthermore, one of 112 hit molecules with a docking score of −10.891 kcal/mol (PIC50 = 10.023 M) was isolated from a study of arginase-I using molecular docking. Protonated ZINC000252286875-linked arginase-1 showed 2.9 RMSD, whereas non-protonated had 1.8. RMSD plots illustrate protein stability in protonated and non-protonated ZINC000252286875-bound states. Protonated-ZINC000252286875-bound proteins contain 25 Rg. The non-protonated protein-ligand combination exhibits a 25.2-Rg, indicating compactness. Protonated and non-protonated ZINC000252286875 stabilised protein targets in binding cavities posthumously. Significant root mean square fluctuations (RMSF) were seen in the arginase-1 protein at a small number of residues for a time function of 500 ns in both the protonated and unprotonated states. Protonated and non-protonated ligands interacted with proteins throughout the simulation. ZINC000252286875 bound Lys64, Asp124, Ala171, Arg222, Asp232, and Gly250. Aspartic acid residue 232 exhibited 200% ionic contact. 500-ns simulations-maintained ions. Salt bridges for ZINC000252286875 aided docking. ZINC000252286875 created six ionic bonds with Lys68, Asp117, His126, Ala171, Lys224, and Asp232 residues. Asp117, His126, and Lys224 showed 200% ionic interactions. In protonated and deprotonated states, GbindvdW, GbindLipo, and GbindCoulomb energies played crucial role. Moreover, ZINC000252286875 meets all of the ADMET standards to serve as a drug. As a result, the current analyses were successful in locating a novel and potent hit molecule that inhibits arginase-I effectively at nanomolar concentrations. The results of this investigation can be used to develop brand-new arginase I inhibitors as an alternative immune-modulating cancer therapy.https://www.frontiersin.org/articles/10.3389/fphar.2023.1129997/fullimmunomodulatoryarginase-iQSARvirtual screeningMD simulation |
| spellingShingle | Magdi E. A. Zaki Sami A. Al-Hussain Aamal A. Al-Mutairi Abdul Samad Arabinda Ghosh Somdatta Chaudhari Pravin N. Khatale Prashant Ajmire Rahul D. Jawarkar In-silico studies to recognize repurposing therapeutics toward arginase-I inhibitors as a potential onco-immunomodulators Frontiers in Pharmacology immunomodulatory arginase-i QSAR virtual screening MD simulation |
| title | In-silico studies to recognize repurposing therapeutics toward arginase-I inhibitors as a potential onco-immunomodulators |
| title_full | In-silico studies to recognize repurposing therapeutics toward arginase-I inhibitors as a potential onco-immunomodulators |
| title_fullStr | In-silico studies to recognize repurposing therapeutics toward arginase-I inhibitors as a potential onco-immunomodulators |
| title_full_unstemmed | In-silico studies to recognize repurposing therapeutics toward arginase-I inhibitors as a potential onco-immunomodulators |
| title_short | In-silico studies to recognize repurposing therapeutics toward arginase-I inhibitors as a potential onco-immunomodulators |
| title_sort | in silico studies to recognize repurposing therapeutics toward arginase i inhibitors as a potential onco immunomodulators |
| topic | immunomodulatory arginase-i QSAR virtual screening MD simulation |
| url | https://www.frontiersin.org/articles/10.3389/fphar.2023.1129997/full |
| work_keys_str_mv | AT magdieazaki insilicostudiestorecognizerepurposingtherapeuticstowardarginaseiinhibitorsasapotentialoncoimmunomodulators AT samiaalhussain insilicostudiestorecognizerepurposingtherapeuticstowardarginaseiinhibitorsasapotentialoncoimmunomodulators AT aamalaalmutairi insilicostudiestorecognizerepurposingtherapeuticstowardarginaseiinhibitorsasapotentialoncoimmunomodulators AT abdulsamad insilicostudiestorecognizerepurposingtherapeuticstowardarginaseiinhibitorsasapotentialoncoimmunomodulators AT arabindaghosh insilicostudiestorecognizerepurposingtherapeuticstowardarginaseiinhibitorsasapotentialoncoimmunomodulators AT somdattachaudhari insilicostudiestorecognizerepurposingtherapeuticstowardarginaseiinhibitorsasapotentialoncoimmunomodulators AT pravinnkhatale insilicostudiestorecognizerepurposingtherapeuticstowardarginaseiinhibitorsasapotentialoncoimmunomodulators AT prashantajmire insilicostudiestorecognizerepurposingtherapeuticstowardarginaseiinhibitorsasapotentialoncoimmunomodulators AT rahuldjawarkar insilicostudiestorecognizerepurposingtherapeuticstowardarginaseiinhibitorsasapotentialoncoimmunomodulators |