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Rebai R, Carmena-Bargueño M, Toumi ME, Derardja I, Jasmin L, Pérez-Sánchez H, Boudah A. Identification of potent inhibitors of kynurenine-3-monooxygenase from natural products: In silico and in vitro approaches. Heliyon 2024; 10:e30287. [PMID: 38726174 PMCID: PMC11079110 DOI: 10.1016/j.heliyon.2024.e30287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/31/2024] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
Existing inhibitors of kynurenine-3-monooxygenase (KMO) have side effects and poorly cross the blood-brain barrier. Therefore, the discovery of new molecules targeting KMO isnecessary.This study aims to develop a novel therapeutic drug targeting KMO using computational methods and experimental validation of natural compounds.The results of our study show that the top four compounds, namely, 3'-Hydroxy-alpha-naphthoflavone exhibited the best docking scores with KMO (-10.0 kcal/mol), followed by 3'-Hydroxy-ss-naphthoflavone (-9.9 kcal/mol), genkwanin (-9.2 kcal/mol) and apigenin(-9.1 kcal/mol) respectively. Molecular dynamics was used to assess the stability of the primary target, KMO, and inhibitor complexes. We found stable interactions of 3'-Hydroxy-ss-naphthoflavone and apigenin with KMO up to 100 ns. Further, kinetic measurements showed that 3'-Hydroxy-alpha-naphthoflavone and 3'-Hydroxy-ss-naphthoflavone induce competitive inhibition with a good IC50 activity (15.85 ± 0.98 μM and 18.71 ± 0.78, respectively), while Genkwanin and Apigenin exhibit non-competitive inhibition mechanism (21.61 ± 0.97 μM and 24.14 ± 1.00 μM, respectively).Drug-likeness features and ADME analysis features also showed that the top four compounds could be used as potential candidates to replace the synthetic KMO inhibitor drugs with known side effects and poor brain-blood barrier penetration.
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Affiliation(s)
- Redouane Rebai
- Department of Natural and Life Sciences, University Mohamed Khider of Biskra, BP 145 RP, 07000, Biskra, Algeria
- Laboratory of biotechnology, National Higher School of Biotechnology, Ville universitaire (university of Constantine 3) Ali Mendjeli, BP E66 25100, Constantine, Algeria
| | - Miguel Carmena-Bargueño
- Structural Bioinformatics and High-Performance Computing Research Group (BIO-HPC), Computer Engineering Department, Universidad Católica de Murcia (UCAM), Campus de los Jerónimos 135, 30107, Guadalupe, Spain
| | - Mohammed Esseddik Toumi
- Laboratory of Microbiological Engineering and Application, Biochemistry and Molecular and Cellular Biology Department, Faculty of Nature and Life Sciences, University of Mentouri Brothers Constantine 1, Constantine, 25017, Algeria
| | - Imene Derardja
- Department of Natural and Life Sciences, University Mohamed Khider of Biskra, BP 145 RP, 07000, Biskra, Algeria
| | - Luc Jasmin
- Department of Oral and Maxillofacial Surgery, University of California, San Francisco, 707 Parnassus Ave Suite D-1201, San Francisco, CA, 94143, USA
| | - Horacio Pérez-Sánchez
- Structural Bioinformatics and High-Performance Computing Research Group (BIO-HPC), Computer Engineering Department, Universidad Católica de Murcia (UCAM), Campus de los Jerónimos 135, 30107, Guadalupe, Spain
| | - Abdennacer Boudah
- Laboratory of biotechnology, National Higher School of Biotechnology, Ville universitaire (university of Constantine 3) Ali Mendjeli, BP E66 25100, Constantine, Algeria
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Mili A, Das S, Nandakumar K, Lobo R. Molecular docking and dynamics guided approach to identify potential anti-inflammatory molecules as NRF2 activator to protect against drug-induced liver injury (DILI): a computational study. J Biomol Struct Dyn 2023; 41:9193-9210. [PMID: 36326112 DOI: 10.1080/07391102.2022.2141885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022]
Abstract
Inflammation and oxidative stress can contribute to the etiology of metabolic and chronic illnesses. The ability to prevent oxidative stress induced diseases such as cancer, cardiovascular disease, Alzheimer's disease, and others has been the subject of global research. Drug-induced liver injury (DILI) pathogenesis can be either due to oxidative stress or inflammatory response elicited by the drug, its metabolite, or herbal supplements. Our present research uses computational studies to identify a molecule with anti-inflammatory properties that can operate as an NRF2 activator. Acquiring and preparing the KEAP1-NRF2 Protein (PDB: 4L7D) with Schrodinger Suite was followed by developing a ligand library (Anti-inflammatory library downloaded from ChemDiv database). Molecular docking studies were performed in HTVS, SP, and XP modes, respectively. Based on the docking score, interaction, ADMET and binding free energy, the top ten compounds were selected and subjected to induced-fit docking (IFD) analysis for further study. The top three molecules were chosen for a molecular dynamics (MD) simulation study. Using the Desmond module of the Schrodinger Suite, the stability of the protein-ligand complex and protein-ligand contact throughout 100ns were evaluated during the MD simulation study. In our study, it was observed that three compounds exhibit exceptional stability and retain the essential interaction throughout the studies, and it is anticipated that these compounds may act as effective NRF2 activators. Further in vitro and in vivo assessments can be conducted to determine its potential to prevent DILI via acting as an NRF2 activator for future drug development.
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Affiliation(s)
- Ajay Mili
- Department of Pharmacognosy, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Subham Das
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Krishnadas Nandakumar
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Richard Lobo
- Department of Pharmacognosy, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
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Bhat NB, Das S, Sridevi BVS, H RC, Nayaka S, S N, Birangal SR, Shenoy GG, Joseph A. Molecular docking and dynamics supported investigation of antiviral activity of Lichen metabolites of Roccella montagnei: an in silico and in vitro study. J Biomol Struct Dyn 2023; 41:11484-11497. [PMID: 36803674 DOI: 10.1080/07391102.2023.2180666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 12/20/2022] [Indexed: 02/22/2023]
Abstract
Lichens are symbiotic organisms that have been traditionally used for treating different kinds of ailments. As there are only a few reports on the antiviral activity of lichens, we thought of evaluating the anti-Herpes simplex virus-1 (HSV-1) activity of methanolic extract of Roccella montagnei and their isolated compounds. Fractionation of crude methanolic extract of Roccella montagnei by column chromatography isolated two pure compounds. Antiviral activity was assessed using a CPE inhibition assay at non-cytotoxic concentrations on Vero cells. Molecular docking and dynamics studies were carried out against Herpes simplex type-1 thymidine kinase to understand the binding interactions of the isolated compounds with reference to acyclovir. Isolated compounds were characterized as methyl orsellinate and montagnetol by spectral methods. Methanolic extract of Roccella montagnei exhibited an EC50 value of 56.51 µg/ml, while the compounds methyl orsellinate and montagnetol offered EC50 values of 13.50 µg/ml and 37.52 µg/ml, respectively, against HSV-1 viral infection on Vero cell lines. The selectively index (SI) of montagnetol (10.93) was found to be higher when compared to that of methyl orsellinate (5.55), indicating its better anti-HSV-1 activity. The docking and dynamics studies showed montagnetol was stable throughout the 100 ns, having better interactions and docking scores with HSV-1 thymidine kinase than methyl orsellinate, as well as the standard. To understand the mechanism of montagnetol's anti-HSV-1 activity, more research is required, and this could lead to the discovery of new and effective antiviral agents.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nishanth B Bhat
- Department of Microbiology, Melaka Manipal Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Subham Das
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Balireddy V S Sridevi
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Raghu Chandrashekhar H
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Sanjeeva Nayaka
- Lichenology Laboratory, CSIR-National Botanical Research Institute, Lucknow, India
| | - Narasimhan S
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Sumit Raosaheb Birangal
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - G Gautham Shenoy
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Alex Joseph
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
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Usmani J, Kausar H, Akbar S, Sartaj A, Mir SR, Hassan MJ, Sharma M, Ahmad R, Rashid S, Ansari MN. Molecular Docking of Bacterial Protein Modulators and Pharmacotherapeutics of Carica papaya Leaves as a Promising Therapy for Sepsis: Synchronising In Silico and In Vitro Studies. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28020574. [PMID: 36677632 PMCID: PMC9862608 DOI: 10.3390/molecules28020574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 12/31/2022] [Accepted: 01/02/2023] [Indexed: 01/09/2023]
Abstract
Sepsis is a serious health concern globally, which necessitates understanding the root cause of infection for the prevention of proliferation inside the host's body. Phytochemicals present in plants exhibit antibacterial and anti-proliferative properties stipulated for sepsis treatment. The aim of the study was to determine the potential role of Carica papaya leaf extract for sepsis treatment in silico and in vitro. We selected two phytochemical compounds, carpaine and quercetin, and docked them with bacterial proteins, heat shock protein (PDB ID: 4PO2), surfactant protein D (PDB ID: 1PW9), and lactobacillus bacterial protein (PDB ID: 4MKS) against imipenem and cyclophosphamide. Quercetin showed the strongest interaction with 1PW9 and 4MKS proteins. The leaves were extracted using ethanol, methanol, and water through Soxhlet extraction. Total flavonoid content, DPPH assay, HPTLC, and FTIR were performed. In vitro cytotoxicity of ethanol extract was screened via MTT assay on the J774 cell line. Ethanol extract (EE) possessed the maximum number of phytocomponents, the highest amount of flavonoid content, and the maximum antioxidant activity compared to other extracts. FTIR analysis confirmed the presence of N-H, O-H, C-H, C=O, C=C, and C-Cl functional groups in ethanol extract. Cell viability was highest (100%) at 25 µg/mL of EE. The present study demonstrated that the papaya leaves possessed antibacterial and cytotoxic activity against sepsis infection.
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Affiliation(s)
- Juveria Usmani
- Department of Pharmacology, School of Pharmaceutical Education and Research, Jamia Hamdard University, New Delhi 110062, India
| | - Hina Kausar
- Department of Pharmacognosy and Phytochemistry, School of Pharmaceutical Education and Research, Jamia Hamdard University, New Delhi 110062, India
| | - Saleem Akbar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard University, New Delhi 110062, India
| | - Ali Sartaj
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard University, New Delhi 110062, India
| | - Showkat R. Mir
- Department of Pharmacognosy and Phytochemistry, School of Pharmaceutical Education and Research, Jamia Hamdard University, New Delhi 110062, India
| | - Mohammed Jaseem Hassan
- Department of Pathology, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh 202002, India
| | - Manju Sharma
- Department of Pharmacology, School of Pharmaceutical Education and Research, Jamia Hamdard University, New Delhi 110062, India
| | - Razi Ahmad
- Department of Pharmacology, Hamdard Institute of Medical Sciences and Research, Jamia Hamdard University, New Delhi 110062, India
- Correspondence: (R.A.); (M.N.A.)
| | - Summaya Rashid
- Department of Pharmacology & Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Mohd Nazam Ansari
- Department of Pharmacology & Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
- Correspondence: (R.A.); (M.N.A.)
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Haider K, Sharma S, Pokharel YR, Das S, Joseph A, Najmi AK, Ahmad F, Yar MS. Synthesis, biological evaluation, and in silico studies of indole-tethered pyrazoline derivatives as anticancer agents targeting topoisomerase IIα. Drug Dev Res 2022; 83:1555-1577. [PMID: 35898169 DOI: 10.1002/ddr.21976] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 11/10/2022]
Abstract
We herein report a new series of indole-tethered pyrazoline derivatives as potent anticancer agents. A total of 12 compounds were designed and synthesized by conventional as well as microwave-irradiated synthesis methods. The latter method results in a significant reduction in the duration of reaction along with improved yields. All synthesized derivatives (7a-7l) were evaluated for their cytotoxic activity against A431, HeLa, and MDAMB-231 cell lines. Compounds 7a and 7b were found most potent in the series and demonstrated an IC50 value of 3.17 and 5.16 µM against the A431 cell line, respectively, compared to the standard drug doxorubicin. Compounds 7a and 7b significantly suppress colony formation, migration, and S phase cell cycle arrest of A431 cells. Furthermore, compound 7a regulated the expression of apoptotic proteins causing the downregulation of procaspase 3/9, antiapoptotic protein Bcl-xL, and upregulation of proapoptotic protein Bax in a dose-dependent manner. Topoisomerase enzyme inhibition assay confirmed that compounds 7a and 7b can significantly inhibit topoisomerase IIα. In vivo oral acute toxicity of compounds 7a and 7b revealed that both compounds are safe compared to doxorubicin; cardiomyopathy studies showed normal architecture of cardiomyocytes and myofibrils. In addition, molecular docking studies revealed the possible interaction of compounds 7a and 7b within the active binding site of the topoisomerase enzyme. The 100 ns molecular dynamic simulation of compounds 7a and 7b proved that both compounds validate all screening parameters.
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Affiliation(s)
- Kashif Haider
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, India
| | - Shivani Sharma
- Faculty of Life Science and Biotechnology, South Asian University, New Delhi, India
| | - Yuba Raj Pokharel
- Faculty of Life Science and Biotechnology, South Asian University, New Delhi, India
| | - Subham Das
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Alex Joseph
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Abul Kalam Najmi
- Department of Pharmacology, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, India
| | - Faiz Ahmad
- Faculty of Life Science and Biotechnology, South Asian University, New Delhi, India
| | - Mohammad Shahar Yar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, India
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Halder D, Das S, R A, R S J. Molecular docking and dynamics based approach for the identification of kinase inhibitors targeting PI3Kα against non-small cell lung cancer: a computational study. RSC Adv 2022; 12:21452-21467. [PMID: 35975074 PMCID: PMC9346375 DOI: 10.1039/d2ra03451d] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 06/23/2022] [Indexed: 12/17/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) is an obscure disease whose incidence is increasing worldwide day by day, and PI3Kα is one of the major targets for cell proliferation due to the mutation. Since PI3K is a class of kinase enzyme, and no in silico research has been performed on the inhibition of PI3Kα mutation by small molecules, we have selected the protein kinase inhibitor database and performed the energy minimization process by ligand preparation. The key objective of this research is to identify the potential hits from the protein kinase inhibitor library and further to perform lead optimization by a molecular docking and dynamics approach. And so, the protein was selected (PDB ID: 4JPS), having a unique inhibitor and a specific binding pocket with amino acid residue for the inhibition of kinase activity. After the docking protocol validation, structure-based virtual screening by molecular docking and MMGBSA binding affinity calculations were performed and a total of ten hits were reported. Detailed analysis of the best scoring molecules was performed with ADMET analysis, induced fit docking (IFD) and molecular dynamics (MD) simulation. Two molecules - 6943 and 34100 - were considered lead molecules and showed better results than the PI3K inhibitor Copanlisib in the docking assessment, ADMET analysis, and molecular dynamics simulation. Furthermore, the synthetic accessibility of the two compounds - 6943 and 34100 - was investigated using SwissADME, and the two lead molecules are easier to synthesize than the PI3K inhibitor Copanlisib. Computational drug discovery tools were used for identification of kinase inhibitors as anti-cancer agents for NSCLC in the present research.
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Affiliation(s)
- Debojyoti Halder
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education Manipal Karnataka-576104 India +919742351531
| | - Subham Das
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education Manipal Karnataka-576104 India +919742351531
| | - Aiswarya R
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education Manipal Karnataka-576104 India +919742351531
| | - Jeyaprakash R S
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education Manipal Karnataka-576104 India +919742351531
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Halder D, Das S, Joseph A, Jeyaprakash RS. Molecular docking and dynamics approach to in silico drug repurposing for inflammatory bowels disease by targeting TNF alpha. J Biomol Struct Dyn 2022; 41:3462-3475. [PMID: 35285757 DOI: 10.1080/07391102.2022.2050948] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Inflammatory bowel disease is a chronic disorder of the large intestine with the prevalence of approximately 400 cases in 100000, and it is rising day by day. However, several drugs like sulfasalazine (composed of sulfapyridine and 5-aminosalicylic acid or 5-ASA), corticosteroids, and immunosuppressants manage the disease. But there are no absolute treatments for the pain and inflammation of the disease. TNFα is an important target, and drugs like infliximab and adalimumab have pharmacological potency but with pronounced toxicity. So, we choose this major target TNFα for the virtual screening of US-FDA-approved drugs for its repurposing using the in silico method. The protein TNFα (PDB ID: 2AZ5) with small molecule inhibitor and the US-FDA-approved drug molecules (from Zinc database) were first imported and prepared using Protein Preparation Wizard and LigPrep, respectively, followed by molecular docking, ADMET analysis and prime MMGBSA. After that, the drugs were shortlisted according to dock score, ADMET parameters and MM GBSA dG binding score. After that, the shortlisted drug molecules were subjected to an induced-fit docking analysis. Two of the most promising molecules, ZINC000003830957 (Iopromide) and ZINC000003830635 (Deferoxamine), were chosen for molecular dynamics simulation. Finally, the bioisosteric replacement was used to improve the ADMET properties of these molecules. This research provides an idea for drug exploration and computational tools for drug discovery in treating inflammatory bowel disease.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Debojyoti Halder
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Subham Das
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Alex Joseph
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - R S Jeyaprakash
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
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