1
|
Dhanabalan AK, Kumar P, Vasudevan S, Chworos A, Velmurugan D. Identification of a novel drug molecule for neurodegenerative disease from marine algae through in-silico analysis. J Biomol Struct Dyn 2024:1-10. [PMID: 38456260 DOI: 10.1080/07391102.2024.2322624] [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: 04/21/2023] [Accepted: 02/16/2024] [Indexed: 03/09/2024]
Abstract
Cognitive functions are lost due to the rapid hydrolysis of acetylcholine including Acetylcholinesterase (AChE) and Butyrylcholinesterase (BChE). Marine algae-derived compounds were reported for their neuroprotective activities and hence they can be utilised for treating neurodegenerative ailments like Alzheimer's Disease and Parkinson's Disease which are due to the loss of cognitive functions. Major attention is currently paid to seaweeds due to their health benefits and high nutritional values. Sea weeds are of a rich sense of natural bioactive compounds which antioxidants, pharmaceutical compounds, flavonoids and alkaloids. They also contain a high amount of vitamins A, D, E, C and Ca, K, Mg and Fe. Regular consumption of a marine algae-based diet may boost immunities. In searching for natural cholinesterase inhibitors, the present study is focussed on some marine bioactive compounds reported from brown, red and green algae. Molecular docking studies have been carried out along with molecular dynamics simulations studies and binding energy calculations resulting in three best bioactive compounds when AChE is used as the target. The results are compared with cocrystal studies. Two best compounds, namely, Diphlorethohydroxycarmalol and Phlorofucofuroeckol from the brown seaweeds are identified as the potential lead compounds for neurodegenerative diseases, Alzheimer's and Parkinson's.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
| | - Praveen Kumar
- Research and Development Cell, AMET University, Kanathur, Tamil Nadu, India
| | - Saranya Vasudevan
- Department of Civil Engineering and Architecture, University of Pavia, Pavia, Italy
| | - Arkadiusz Chworos
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies Polish Academy of Sciences, Lodz, Poland
| | - Devadasan Velmurugan
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
| |
Collapse
|
2
|
Kumar M, Parveen, Raj N, Khatoon S, Fakhri KU, Kumar P, Alamri MA, Kamal M, Manzoor N, Harsha, Solanki R, Elossaily GM, Asiri YI, Hassan MZ, Kapur MK. In-silico and in-vitro evaluation of antifungal bioactive compounds from Streptomyces sp. strain 130 against Aspergillus flavus. J Biomol Struct Dyn 2024:1-19. [PMID: 38319066 DOI: 10.1080/07391102.2024.2313167] [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: 07/17/2023] [Accepted: 01/25/2024] [Indexed: 02/07/2024]
Abstract
Streptomyces spp. are considered excellent reservoirs of natural bioactive compounds. The study evaluated the bioactive potential of secondary metabolites from Streptomyces sp. strain 130 through PKS-I and NRPS gene-clusters screening. GC-MS analysis was done for metabolic profiling of bioactive compounds from strain 130 in the next set of experiments. Identified antifungal compounds underwent ADMET analyses to screen their toxicity. All compounds' molecular docking was done with the structural gene products of the aflatoxin biosynthetic pathway of Aspergillus flavus. MD simulations were utilized to evaluate the stability of protein-ligand complexes under physiological conditions. Based on the in-silico studies, compound 2,4-di-tert butyl-phenol (DTBP) was selected for in-vitro studies against Aspergillus flavus. Simultaneously, bioactive compounds were extracted from strain 130 in two different solvents (ethyl-acetate and methanol) and used for similar assays. The MIC value of DTBP was found to be 314 µg/mL, whereas in ethyl-acetate extract and methanol-extract, it was 250 and 350 µg/mL, respectively. A mycelium growth assay was done to analyze the effect of compounds/extracts on the mycelium formation of Aspergillus flavus. In agar diffusion assay, zone of inhibitions in DTBP, ethyl-acetate extract, and methanol extract were observed with diameters of 11.3, 13.3, and 7.6 mm, respectively. In the growth curve assay, treated samples have delayed the growth of fungi, which signified that the compounds have a fungistatic nature. Spot assay has determined the fungal sensitivity to a sub-minimum inhibitory concentration of antifungal compounds. The study's results suggested that DTBP can be exploited for antifungal-drug development.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Munendra Kumar
- Department of Zoology, Rajiv Gandhi University, Doimukh, India
| | - Parveen
- Medical Mycology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Nafis Raj
- Medical Mycology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Shabana Khatoon
- Medical Mycology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | | | - Prateek Kumar
- Department of Zoology, University of Allahabad, Prayagraj, India
| | - Mubarak A Alamri
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Mehnaz Kamal
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Nikhat Manzoor
- Medical Mycology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Harsha
- Microbial Technology Lab, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, India New Delhi
| | - Renu Solanki
- Deen Dayal Upadhyaya College, University of Delhi, New Delhi, India
| | - Gehan M Elossaily
- Department of Basic Medical Sciences, College of Medicine, AlMaarefa University, Riyadh, Saudi Arabia
| | - Yahya I Asiri
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Mohd Zaheen Hassan
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Monisha Khanna Kapur
- Microbial Technology Lab, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, India New Delhi
| |
Collapse
|
3
|
Swati K, Varma SR, Parameswari RP, Panda SP, Agrawal M, Prakash A, Kumar D, Agarwal P. Computational exploration of FOXM1 inhibitors for glioblastoma: an integrated virtual screening and molecular dynamics simulation study. J Biomol Struct Dyn 2024:1-19. [PMID: 38305824 DOI: 10.1080/07391102.2024.2308772] [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: 10/03/2023] [Accepted: 01/14/2024] [Indexed: 02/03/2024]
Abstract
In this study, a comprehensive investigation of a set of phytochemicals to identify potential inhibitors for the Forkhead box protein M1 (FOXM1) was conducted. FOXM1 is overexpressed in glioblastoma (GBM) cells and plays a crucial role in cell cycle progression, proliferation, and invasion. FOXM1 inhibitors have shown promising results in preclinical studies, and ongoing clinical trials are assessing their efficacy in GBM patients. However, there are limited studies on the identification of novel compounds against this attractive therapeutic target. To address this, the NPACT database containing 1,574 phytochemicals was used, employing a hierarchical multistep docking approach, followed by an estimation of relative binding free energy. By fixing user-defined XP-dock and MM-GBSA cut-off scores of -6.096 and -37.881 kcal/mol, the chemical space was further narrowed. Through exhaustive analysis of molecular binding interactions and various pharmacokinetics profiles, we identified four compounds, namely NPACT00002, NPACT01454, NPACT00856, and NPACT01417, as potential FOXM1 inhibitors. To assess the stability of protein-ligand binding in dynamic conditions, 100 ns Molecular dynamics (MD) simulations studies were performed. Furthermore, Molecular mechanics with generalized Born and surface area solvation (MM-GBSA) based binding free energy estimations of the entire simulation trajectories revealed a strong binding affinity of all identified compounds towards FOXM1, surpassing that of the control drug Troglitazone. Based on extensively studied multistep docking approaches, we propose that these molecules hold promise as FOXM1 inhibitors for potential therapeutic applications in GBM. However, experimental validation will be necessary to confirm their efficacy as targeted therapies.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Kumari Swati
- Department of Biotechnology, School of Life Science, Mahatma Gandhi Central University, Motihari, Bihar, India
| | - Sudhir Rama Varma
- Department of clinical sciences, Centre for Medical and Bioallied Health Sciences Research, Ajman university, Ajman, UAE
| | - R P Parameswari
- Center for Global Health Research, Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | - Siva Prasad Panda
- Institute of Pharmaceutical Research, GLA University, Mathura, Uttar Pradesh, India
| | - Mohit Agrawal
- School of Medical & Allied Sciences, K.R. Mangalam University, Gurugram, Haryana, India
| | - Anand Prakash
- Department of Biotechnology, School of Life Science, Mahatma Gandhi Central University, Motihari, Bihar, India
| | - Dhruv Kumar
- School of Health Sciences and Technology, UPES, Dehradun, Uttrakhand, India
| | - Prasoon Agarwal
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Division of Occupational and Environmental Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
| |
Collapse
|
4
|
Naik HN, Kanjariya D, Parveen S, Ahmed I, Meena A, Patel H, Meena R, Jauhari S. LC-MS profiling, in vitro and in silico C-ABL kinase inhibitory approach to identify potential anticancer agents from Dalbergia sissoo leaves. Sci Rep 2024; 14:73. [PMID: 38167560 PMCID: PMC10761914 DOI: 10.1038/s41598-023-49995-1] [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: 08/11/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
Belonging to the Fabaceae family, Dalbergia sissoo, a versatile plant, has gained prominence for its potent medicinal attributes, especially antipyretic, anti-inflammatory, and cardioprotective properties, as well as the use of its leaf juice in cancer treatment. Despite these recognized applications by natives and tribals, comprehensive insight into its biological activities and chemical composition remains limited. This study aimed to explore the cytotoxic potential of sequentially extracted leaf extracts from Dalbergia sissoo using various solvents, aiming to unveil the array of phytochemicals through LC-MS profiling. Among the extracts evaluated, the extract employing methanol:water extracting media (HN-2) appeared with the most remarkable results in both phytochemical diversity and biological activity. Furthermore, in vitro results of HN-2's in vitro anticancer efficacy were confirmed through in silico molecular docking and molecular dynamics simulation. These analyses demonstrated its ability to inhibit C-ABL kinase within leukemia K562 cells, directing that Dalbergia sissoo leaves serve as a bioactive agent reservoir. Consequently, this suggests that the Dalbergia sissoo plant is a potential source of bioactive compounds that can be used as a precursor for developing new cancer inhibitors, mainly targeting leukemia.
Collapse
Affiliation(s)
- Hem N Naik
- Department of Chemistry, SV National Institute of Technology, Surat, Gujarat, 395007, India
| | - Dilip Kanjariya
- Department of Chemistry, SV National Institute of Technology, Surat, Gujarat, 395007, India
| | - Shahnaz Parveen
- Molecular Bioprospection Department, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, 226015, India
| | - Iqrar Ahmed
- Department of Pharmaceutical Chemistry, Prof. Ravindra Nikam College of Pharmacy, Gondur, Dhule, Maharashtra, 424002, India
| | - Abha Meena
- Molecular Bioprospection Department, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, 226015, India
| | - Harun Patel
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R.C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, 425405, India
| | - Ramavatar Meena
- Natural Product and Green Chemistry Division, CSIR-Central Salt & Marine Chemicals Research Institute, G. B. Marg, Bhavnagar, Gujarat, 364002, India
| | - Smita Jauhari
- Department of Chemistry, SV National Institute of Technology, Surat, Gujarat, 395007, India.
| |
Collapse
|
5
|
Noumi E, Ahmad I, Adnan M, Patel H, Merghni A, Haddaji N, Bouali N, Alabbosh KF, Kadri A, Caputo L, Polito F, Snoussi M, Feo VD. Illicium verum L. (Star Anise) Essential Oil: GC/MS Profile, Molecular Docking Study, In Silico ADME Profiling, Quorum Sensing, and Biofilm-Inhibiting Effect on Foodborne Bacteria. Molecules 2023; 28:7691. [PMID: 38067422 PMCID: PMC10707387 DOI: 10.3390/molecules28237691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/09/2023] [Accepted: 11/14/2023] [Indexed: 12/18/2023] Open
Abstract
Illicium verum, or star anise, has many uses ranging from culinary to religious. It has been used in the food industry since ancient times. The main purpose of this study was to determine the chemical composition, antibacterial, antibiofilm, and anti-quorum sensing activities of the essential oil (EO) obtained via hydro-distillation of the aerial parts of Illicium verum. Twenty-four components were identified representing 92.55% of the analyzed essential oil. (E)-anethole (83.68%), limonene (3.19%), and α-pinene (0.71%) were the main constituents of I. verum EO. The results show that the obtained EO was effective against eight bacterial strains to different degrees. Concerning the antibiofilm activity, trans-anethole was more effective against biofilm formation than the essential oil when tested using sub-inhibitory concentrations. The results of anti-swarming activity tested against P. aeruginosa PAO1 revealed that I. verum EO possesses more potent inhibitory effects on the swarming behavior of PAO1 when compared to trans-anethole, with the percentage reaching 38% at a concentration of 100 µg/mL. The ADME profiling of the identified phytocompounds confirmed their important pharmacokinetic and drug-likeness properties. The in silico study using a molecular docking approach revealed a high binding score between the identified compounds with known target enzymes involved in antibacterial and anti-quorum sensing (QS) activities. Overall, the obtained results suggest I. verum EO to be a potentially good antimicrobial agent to prevent food contamination with foodborne pathogenic bacteria.
Collapse
Affiliation(s)
- Emira Noumi
- Department of Biology, College of Science, University of Hail, P.O. Box 2440, Ha’il 2440, Saudi Arabia; (M.A.); (N.H.); (N.B.); (K.F.A.); (M.S.)
- Laboratory of Genetics, Biodiversity and Valorization of Bio-Resources (LR11ES41), Higher Institute of Biotechnology of Monastir, University of Monastir, Avenue Tahar Haddad, BP74, Monastir 5000, Tunisia
| | - Iqrar Ahmad
- Department of Pharmaceutical Chemistry, Prof. Ravindra Nikam College of Pharmacy, Gondur, Dhule 424002, Maharashtra, India;
| | - Mohd Adnan
- Department of Biology, College of Science, University of Hail, P.O. Box 2440, Ha’il 2440, Saudi Arabia; (M.A.); (N.H.); (N.B.); (K.F.A.); (M.S.)
| | - Harun Patel
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur 425405, Maharashtra, India;
| | - Abderrahmen Merghni
- Laboratory of Antimicrobial Resistance LR99ES09, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis 1068, Tunisia;
| | - Najla Haddaji
- Department of Biology, College of Science, University of Hail, P.O. Box 2440, Ha’il 2440, Saudi Arabia; (M.A.); (N.H.); (N.B.); (K.F.A.); (M.S.)
| | - Nouha Bouali
- Department of Biology, College of Science, University of Hail, P.O. Box 2440, Ha’il 2440, Saudi Arabia; (M.A.); (N.H.); (N.B.); (K.F.A.); (M.S.)
| | - Khulood Fahad Alabbosh
- Department of Biology, College of Science, University of Hail, P.O. Box 2440, Ha’il 2440, Saudi Arabia; (M.A.); (N.H.); (N.B.); (K.F.A.); (M.S.)
| | - Adel Kadri
- College of Science and Arts in Baljurashi, Al-Baha University, P.O. Box 1988, Al Baha 65527, Saudi Arabia;
| | - Lucia Caputo
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy; (L.C.); (F.P.)
| | - Flavio Polito
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy; (L.C.); (F.P.)
| | - Mejdi Snoussi
- Department of Biology, College of Science, University of Hail, P.O. Box 2440, Ha’il 2440, Saudi Arabia; (M.A.); (N.H.); (N.B.); (K.F.A.); (M.S.)
- Laboratory of Genetics, Biodiversity and Valorization of Bio-Resources (LR11ES41), Higher Institute of Biotechnology of Monastir, University of Monastir, Avenue Tahar Haddad, BP74, Monastir 5000, Tunisia
| | - Vincenzo De Feo
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy; (L.C.); (F.P.)
| |
Collapse
|
6
|
Kanjariya DC, Naik HN, Sherashiya MJ, Naliapara YT, Ahmad I, Patel H, Rajani D, Jauhari S. α-Amylase and mycobacterium-TB H37Rv antagonistic efficacy of novel pyrazole-coumarin hybrids: an in vitro and in silico investigation. J Biomol Struct Dyn 2023:1-18. [PMID: 37904535 DOI: 10.1080/07391102.2023.2273436] [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: 07/26/2023] [Accepted: 10/15/2023] [Indexed: 11/01/2023]
Abstract
The present investigation of minutiae to acquire structural information of the novel pyrazole-coumarin hybrids (PC1-PC10) synthesized using ultrasound methods and characterized using different spectroscopic techniques: mass, 1H-NMR, 13 C-NMR and IR spectroscopy, and theoretically explored using the DFT approach with a B3LYP/6-311G (d, p) basis set, and there in vitro, antagonistic efficacy against α-amylase and mycobacterium-TB H37Rv are described in this article. Pyrazole-coumarin hybrids (PC1-PC10) showed α-amylase inhibition ranging from IC50 (0.32-0.58 mM) when compared with acarbose (IC50 = 0.34 mM). Similarly, Mycobacterium-TB H37Rv strain inhibition screening showed MIC values ranging from 62.5 to 1000 µg/mL when compared with rifampicin and isoniazid MIC = 0.25 and 0.20 µg/mL, respectively. Molecular docking and MD simulation studies were performed to determine the active sites and rationalize the activities of the active compounds. To investigate the binding conformation and dynamics responsible for their activity, the three most active compounds (PC1, PC3 and PC6) were docked into the porcine pancreatic α-amylase active site (PDB ID:1OSE), and mycobacterium-TB H37Rv active site (PDB ID: 4TZK). The binding interactions between PC1, PC3, and PC6 with α-amylase were like those responsible for inhibiting α-amylase by acarbose. Also, the mycobacterium-TB H37Rv inhibiting responsible residues were compared with standard isoniazid and rifampicin.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Dilip C Kanjariya
- Department of Chemistry, Sardar Vallabhbhai National Institute of Technology, Surat, India
| | - Hem N Naik
- Department of Chemistry, Sardar Vallabhbhai National Institute of Technology, Surat, India
| | | | | | - Iqrar Ahmad
- Department of Pharmaceutical Chemistry, Prof. Ravindra Nikam College of Pharmacy, Dhule, India
| | - Harun Patel
- Department of Pharmaceutical Chemistry, Division of Computer Aided Drug Design, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, India
| | - Dhanji Rajani
- Microcare Laboratory and Tuberculosis Research Center, Surat, India
| | - Smita Jauhari
- Department of Chemistry, Sardar Vallabhbhai National Institute of Technology, Surat, India
| |
Collapse
|