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Mahnashi MH, Nahari M, Almasoudi H, Alhasaniah A, Elgazwi S, Abou-Salim MA. Novel NO-TZDs and trimethoxychalcone-based DHPMs: design, synthesis, and biological evaluation as potential VEGFR-2 inhibitors. J Enzyme Inhib Med Chem 2024; 39:2358934. [PMID: 38904116 PMCID: PMC467104 DOI: 10.1080/14756366.2024.2358934] [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: 01/19/2024] [Accepted: 05/19/2024] [Indexed: 06/22/2024] Open
Abstract
Novel series of nitric oxide-releasing thiazolidine-2,4-diones (NO-TZD-3a-d,5,6) and 3,4,5-trimethoxychalcone-based multifunctional 1,4-dihydropyrimidines (CDHPM-10a-g) have been designed and synthesised as potent broad-spectrum anticancer agents with potential VEGFR-2 inhibition. The designed analogs were evaluated for their anticancer activities towards a full panel of NCI-60 tumour cell lines and CDHPM-10a-g emerged mean %inhibitions ranging from 76.40 to 147.69%. Among them, CDHPM-10e and CDHPM-10f demonstrated the highest MGI% of 147.69 and 140.24%, respectively. Compounds CDHPM-10a,b,d-f showed higher mean %inhibitory activity than the reference drug sorafenib (MGI% = 105.46%). Superiorly, the hybrid CDHPM-10e displayed the highest potencies towards all the herein tested subpanels of nine types of cancer with MGI50 of 1.83 µM. Also, it revealed potent cytostatic single-digit micromolar activity towards the herein examined cancer cell lines. The designed compounds CDHPM-10a-g were exposed as potent non-selective broad-spectrum anticancer agents over all NCI subpanels with an SI range of 0.66-1.97. In addition, the target analog CDHPM-10e revealed potency towards VEGFR-2 kinase comparable to that of sorafenib with a sub-micromolar IC50 value of 0.11 µM. Also, CDHPM-10e could effectively induce Sub-G1-phase arrest and prompt apoptosis via caspase and p53-dependent mechanisms. Furthermore, CDHPM-10e revealed significant anti-metastatic activity as detected by wound healing assay. The modelling study implies that CDHPM-10e overlaid well with sorafenib and formed a strong H-bond in the DFG binding domain. The ADMET studies hinted out that CDHPM-10e met Pfizer's drug-likeness criteria. The presented novel potent anticancer agent merits further devotion as a new lead product in developing more chalcone-based VEGFR-2 inhibitors.
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Affiliation(s)
- Mater H. Mahnashi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Najran University, Najran, Saudi Arabia
| | - Mohammed Nahari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Hassan Almasoudi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Abdulaziz Alhasaniah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Sara Elgazwi
- Department of Chemistry, University of Derna, Derna, Libya
| | - Mahrous A. Abou-Salim
- Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Al-Azhar University, Assiut, Egypt
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Coelho MM, Lima R, Almeida AS, Fernandes PA, Remião F, Fernandes C, Tiritan ME. Binding studies of promethazine and its metabolites with human serum albumin by high-performance affinity chromatography and molecular docking in the presence of codeine. Anal Bioanal Chem 2024; 416:4605-4618. [PMID: 38965103 PMCID: PMC11294390 DOI: 10.1007/s00216-024-05409-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 06/08/2024] [Accepted: 06/14/2024] [Indexed: 07/06/2024]
Abstract
"Purple Drank", a soft drink containing promethazine (PMZ) and codeine (COD), has gained global popularity for its hallucinogenic effects. Consuming large amounts of this combination can lead to potentially fatal events. The binding of these drugs to plasma proteins can exacerbate the issue by increasing the risk of drug interactions, side effects, and/or toxicity. Herein, the binding affinity to human serum albumin (HSA) of PMZ and its primary metabolites [N-desmethyl promethazine (DMPMZ) and promethazine sulphoxide (PMZSO)], along with COD, was investigated by high-performance affinity chromatography (HPAC) though zonal approach. PMZ and its metabolites exhibited a notable binding affinity for HSA (%b values higher than 80%), while COD exhibited a %b value of 65%. To discern the specific sites of HSA to which these compounds were bound, displacement experiments were performed using warfarin and (S)-ibuprofen as probes for sites I and II, respectively, which revealed that all analytes were bound to both sites. Molecular docking studies corroborated the experimental results, reinforcing the insights gained from the empirical data. The in silico data also suggested that competition between PMZ and its metabolites with COD can occur in both sites of HSA, but mainly in site II. As the target compounds are chiral, the enantioselectivity for HSA binding was also explored, showing that the binding for these compounds was not enantioselective.
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Affiliation(s)
- Maria Miguel Coelho
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy of the University of Porto, 4050-313, Porto, Portugal
- CIIMAR-Interdisciplinary Center for Marine and Environmental Research University of Porto, Porto de Leixões Cruise Terminal, 4450-208, Matosinhos, Portugal
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313, Porto, Portugal
| | - Rita Lima
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy of the University of Porto, 4050-313, Porto, Portugal
- CIIMAR-Interdisciplinary Center for Marine and Environmental Research University of Porto, Porto de Leixões Cruise Terminal, 4450-208, Matosinhos, Portugal
| | - Ana Sofia Almeida
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy of the University of Porto, 4050-313, Porto, Portugal
- CIIMAR-Interdisciplinary Center for Marine and Environmental Research University of Porto, Porto de Leixões Cruise Terminal, 4450-208, Matosinhos, Portugal
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313, Porto, Portugal
| | - Pedro Alexandrino Fernandes
- LAQV, REQUIMTE, Departamento de Química E Bioquímica, Faculdade de Ciências, Universidade Do Porto, Rua Do Campo Alegre, S/N, 4169-007, Porto, Portugal
| | - Fernando Remião
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313, Porto, Portugal
| | - Carla Fernandes
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy of the University of Porto, 4050-313, Porto, Portugal.
- CIIMAR-Interdisciplinary Center for Marine and Environmental Research University of Porto, Porto de Leixões Cruise Terminal, 4450-208, Matosinhos, Portugal.
| | - Maria Elizabeth Tiritan
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy of the University of Porto, 4050-313, Porto, Portugal.
- CIIMAR-Interdisciplinary Center for Marine and Environmental Research University of Porto, Porto de Leixões Cruise Terminal, 4450-208, Matosinhos, Portugal.
- 1H-TOXRUN - One Health Toxicology Research Unit, University Institute of Health Sciences (IUCS), CESPU, CRL, 4585-116, Gandra, Portugal.
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Sakander N, Ahmed A, Bhardwaj M, Kumari D, Nandi U, Mukherjee D. A path from synthesis to emergency use authorization of molnupiravir as a COVID-19 therapy. Bioorg Chem 2024; 147:107379. [PMID: 38643567 DOI: 10.1016/j.bioorg.2024.107379] [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: 12/26/2023] [Revised: 04/04/2024] [Accepted: 04/14/2024] [Indexed: 04/23/2024]
Abstract
Coronaviruses are a group of enveloped viruses with non-segmented, single-stranded, and positive-sense RNA genomes. It belongs to the 'Coronaviridae family', responsible for various diseases, including the common cold, SARS, and MERS. The COVID-19 pandemic, which began in March 2020, has affected 209 countries, infected over a million people, and claimed over 50,000 lives. Significant efforts have been made by repurposing several approved drugs including antiviral, to combat the COVID-19 pandemic. Molnupiravir is found to be the first orally acting efficacious drug to treat COVID-19 cases. It was approved for medical use in the UK in November 2021 and other countries, including USFDA, which granted approval an emergency use authorization (EUA) for treating adults with mild to moderate COVID-19 patients. Considering the importance of molnupiravir, the present review deals with its various synthetic strategies, pharmacokinetics, bio-efficacy, toxicity, and safety profiles. The comprehensive information along with critical analysis will be very handy for a wide range of audience including medicinal chemists in the arena of antiviral drug discovery especially anti-viral drugs against any variant of COVID-19.
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Affiliation(s)
- Norein Sakander
- Natural Product and Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ajaz Ahmed
- Natural Product and Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Mahir Bhardwaj
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India
| | - Diksha Kumari
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Infectious Diseases Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India
| | - Utpal Nandi
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India
| | - Debaraj Mukherjee
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Department of Chemical Sciences, Bose Institute, EN 80, Sector V, Bidhan Nagar, Kolkata 700091, WB, India.
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Rahman MS, Hosen ME, Faruqe MO, Khalekuzzaman M, Islam MA, Acharjee UK, Bin Jardan YA, Nafidi HA, Mekonnen AB, Bourhia M, Zaman R. Evaluation of Adenanthera pavonina-derived compounds against diabetes mellitus: insight into the phytochemical analysis and in silico assays. Front Mol Biosci 2024; 10:1278701. [PMID: 38601799 PMCID: PMC11004346 DOI: 10.3389/fmolb.2023.1278701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 12/19/2023] [Indexed: 04/12/2024] Open
Abstract
Adenanthera pavonina is a medicinal plant with numerous potential secondary metabolites showing a significant level of antidiabetic activity. The objective of the current study was to identify potential phytochemicals from the methanolic leaf extract of Adenanthera pavonina as therapeutic agents against diabetes mellitus using GC-MS and in silico methods. The GC-MS analysis of the leaf extract revealed a total of 17 phytochemicals. Molecular docking was performed using these phytochemicals, targeting the mutated insulin receptor tyrosine kinase (5hhw), which inhibits glucose uptake by cells. Diazoprogesterone (-9.2 kcal/mol), 2,4,4,7a-Tetramethyl-1-(3-oxobutyl)octahydro-1H-indene-2-carboxylic acid (-6.9 kcal/mol), and 2-Naphthalenemethanol, decahydro-.alpha.,.alpha.,4a-trimethyl-8-methylene-, [2R-(2.alpha.,4a.alpha.,8a.beta.)] (-6.6 kcal/mol) exhibited better binding with the target protein. The ADMET analysis was performed for the top three compounds with the best docking scores, which showed positive results with no observed toxicity in the AMES test. Furthermore, the molecular dynamics study confirmed the favorable binding of Diazoprogesterone, 2,4,4,7a-Tetramethyl-1-(3-oxobutyl)octahydro-1H-indene-2-carboxylic acid and 2-Naphthalenemethanol, decahydro-.alpha.,.alpha.,4a-trimethyl-8-methylene-, [2R-(2.alpha.,4a.alpha.,8a.beta.)] with the receptor throughout the 100 ns simulation period.
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Affiliation(s)
- Md. Sojiur Rahman
- Professor Joarder DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Eram Hosen
- Professor Joarder DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Omar Faruqe
- Department of Computer Science and Engineering, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Khalekuzzaman
- Professor Joarder DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Asadul Islam
- Professor Joarder DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Uzzal Kumar Acharjee
- Professor Joarder DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Yousef A. Bin Jardan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Hiba-Allah Nafidi
- Department of Food Science, Faculty of Agricultural and Food Sciences, Laval University, Quebec City, QC, Canada
| | | | - Mohammed Bourhia
- Laboratory of Biotechnology and Natural Resources Valorization, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco
| | - Rashed Zaman
- Professor Joarder DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
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Khadri MJN, Ramu R, Simha NA, Khanum SA. Synthesis, molecular docking, analgesic, anti-inflammatory, and ulcerogenic evaluation of thiophene-pyrazole candidates as COX, 5-LOX, and TNF-α inhibitors. Inflammopharmacology 2024; 32:693-713. [PMID: 37985602 DOI: 10.1007/s10787-023-01364-0] [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: 09/01/2023] [Accepted: 10/02/2023] [Indexed: 11/22/2023]
Abstract
The thiophene bearing pyrazole derivatives (7a-j) were synthesized and examined for their in vitro cyclooxygenase, 5-lipoxygenase, and tumour inducing factor-α inhibitory activities followed by the in vivo analgesic, anti-inflammatory, and ulcerogenic evaluations. The synthesized series (7a-j) were characterized using 1H NMR, 13C NMR, FT-IR, and mass spectral analysis. Initially, the compounds (7a-j) were evaluated for their in vitro cyclooxygenase, 5-lipoxygenase, and tumour inducing factor-α inhibitory activities and the compound (7f) with two phenyl substituents in the pyrazole ring and chloro substituent in the thiophene ring and the compound (7g) with two phenyl substituents in the pyrazole ring and bromo substituent in the thiophene ring were observed as potent compounds among the series. The compounds (7f and 7g) with effective in vitro potentials were further analyzed for analgesic, anti-inflammatory, and ulcerogenic evaluations. Also, to ascertain the binding affinities of compounds (7a-j), docking assessments were carried out and the ligand (7f) with the highest binding affinity was docked to know the interactions of the ligand with amino acids of target proteins.
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Affiliation(s)
- M J Nagesh Khadri
- Department of Chemistry, Yuvaraja's College (Autonomous), University of Mysore, Mysuru, Karnataka, 570005, India
| | - Ramith Ramu
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education & Research, Mysuru, Karnataka, 570015, India
| | - N Akshaya Simha
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education & Research, Mysuru, Karnataka, 570015, India
| | - Shaukath Ara Khanum
- Department of Chemistry, Yuvaraja's College (Autonomous), University of Mysore, Mysuru, Karnataka, 570005, India.
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Hassan AMS, Elfiky AA, Elgohary AM. Triple in silico targeting of IMPDH enzyme and RNA-dependent RNA polymerase of both SARS-CoV-2 and Rhizopus oryzae. Future Microbiol 2024; 19:9-19. [PMID: 38294272 DOI: 10.2217/fmb-2023-0103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 08/23/2023] [Indexed: 02/01/2024] Open
Abstract
Aim: Mucormycosis has been associated with SARS-CoV-2 infections during the last year. The aim of this study was to triple-hit viral and fungal RNA-dependent RNA polymerases (RdRps) and human inosine monophosphate dehydrogenase (IMPDH). Materials & methods: Molecular docking and molecular dynamics simulation were used to test nucleotide inhibitors (NIs) against the RdRps of SARS-CoV-2 and Rhizopus oryzae RdRp. These same inhibitors targeted IMPDH. Results: Four NIs revealed a comparable binding affinity to the two drugs, remdesivir and sofosbuvir. Binding energies were calculated using the most abundant conformations of the RdRps after 100-ns molecular dynamics simulation. Conclusion: We suggest the triple-inhibition potential of four NIs against pathogenic RdRps and IMPDH, which is worth experimental validation.
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Affiliation(s)
| | - Abdo A Elfiky
- Biophysics Department, Faculty of Sciences, Cairo University, Giza, Dokki, 12613, Egypt
| | - Alaa M Elgohary
- Biophysics Department, Faculty of Sciences, Cairo University, Giza, Dokki, 12613, Egypt
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Ghedira D, El Harran AA, Abderrazak H. Design and study of bioisosteric analogues of the drug Molnupiravir as potential therapeutics against SARS-COV-2: an in silico approach. In Silico Pharmacol 2023; 12:1. [PMID: 38050480 PMCID: PMC10693539 DOI: 10.1007/s40203-023-00171-3] [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: 07/25/2023] [Accepted: 10/12/2023] [Indexed: 12/06/2023] Open
Abstract
The ongoing SARS-CoV-2 pandemic has created an urgent need for effective antiviral drugs that can be rapidly developed and utilized to treat patients infected with the virus. Molnupiravir, a direct-acting oral antiviral, has shown promising results in reducing viral infections with SARS-CoV-2. Nonetheless, there is still a need for the development of more efficacious analogues with enhanced interaction with the specific target, the RNA dependent RNA polymerase (RdRp) and better physico-chemical profile. Our study is based on a rational design strategy, known as "bioisosterism", to design some analogues. The pool of bioisosteric structural analogues was further enriched using the "SwissBioisostere" database. Only structures with a Tanimoto score more than 0.85 (calculated using the Maximum Common Substructure scoring method) and with ΔlogP (lipophilicity) ± 1 and ΔPSA (Polar Surface Area) ± 10 Å were retained. Next, molecular docking studies were conducted using AutoDock Vina®. Ligand and receptor preparation and molecular interaction analysis were performed using UCSF Chimera® and Biovia Discovery Studio®, respectively. The three-dimensional structure of the RdRp of SARS-CoV-2 (6M71) was sourced from RCSB PDB®. Ligands were prepared in 3D, and the receptor underwent solvent removal, elimination of alternative positions, hydrogen atom addition, and partial charge assignment. Binding pocket coordinates were determined, and utilized for AutoDock Vina® docking. Parallelly, the druglikeness of our molecules was predicted using the website ADME-SWISS: http://www.swissadme.ch/, based on Lipinski and Weber scores. Docking outcomes, combined to druglikeness prediction results, identified two fluorinated analogues with superior binding affinity (lowest score and an RMSD ≤ 2 Å) and improved physico-chemical properties (no violation of Lipinsky and Veber rules). This study contributes to the development of more effective antiviral drugs by providing insights into potential uegs with enhanced interactions with RNA polymerase and better druglikeness profile. Graphical abstract
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Affiliation(s)
- Donia Ghedira
- Present Address: Laboratory of Drugs Development (LR12ES09), Faculty of Pharmacy of Monastir, Monastir, Tunisia
| | - Abderrazak Aziz El Harran
- Present Address: Laboratory of Drugs Development (LR12ES09), Faculty of Pharmacy of Monastir, Monastir, Tunisia
| | - Houyem Abderrazak
- Laboratory of Useful Materials (LMU), National Institute of Research and Physico-Chemical Analysis (INRAP), Sidi Thabet, Tunisia
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Mahnashi M, Alshahrani MM, Al Ali A, Asiri A, Abou-Salim MA. Novel Glu-based pyrazolo[3,4-d]pyrimidine analogues: design, synthesis and biological evaluation as DHFR and TS dual inhibitors. J Enzyme Inhib Med Chem 2023; 38:2203879. [PMID: 37080777 PMCID: PMC10120551 DOI: 10.1080/14756366.2023.2203879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
A novel series of multifunctional pyrazolo[3,4-d]pyrimidine-based glutamate analogs (6a-l and 7a,b) have been designed and synthesized as antifolate anticancer agents. Among the tested compounds, 6i exhibited the most potent anti-proliferative activity towards NSCLC, CNS, Ovarian, Prostate, Colon, Melanoma, Breast, and Renal cancers with good to weak cytostatic activity and non-lethal actions. 6i demonstrated higher selectivity for cancer than normal cells. 6i could significantly increase the accumulation of S-phase cells during the cell cycle distribution of cancer cells with high potency in the induction of apoptosis. The results unveiled that 6i probably acts through dual inhibition of DHFR and TS enzymes (IC50 = 2.41 and 8.88 µM, correspondingly). Docking studies of 6i displayed that N1-p-bromophenyl and C3-Methyl groups participate in substantial hydrophobic interactions. The drug-likeness features inferred that 6i met the acceptance criteria of Pfizer. Taking together, 6i could be a promising prototype for further optimization as an effective anticancer drug.
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Affiliation(s)
- Mater Mahnashi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Najran University, Najran, Saudi Arabia
| | - Mohammed Merae Alshahrani
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Amer Al Ali
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, University of Bisha, Bisha, Saudi Arabia
| | - Abdulaziz Asiri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, University of Bisha, Bisha, Saudi Arabia
| | - Mahrous A Abou-Salim
- Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Al-Azhar University, Assiut, Egypt
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Pradeep S, Patil SM, Dharmashekara C, Jain A, Ramu R, Shirahatti PS, Mandal SP, Reddy P, Srinivasa C, Patil SS, Ortega-Castro J, Frau J, Flores-Holgúın N, Shivamallu C, Kollur SP, Glossman-Mitnik D. Molecular insights into the in silico discovery of corilagin from Terminalia chebula as a potential dual inhibitor of SARS-CoV-2 structural proteins. J Biomol Struct Dyn 2023; 41:10869-10884. [PMID: 36576118 DOI: 10.1080/07391102.2022.2158943] [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: 08/03/2022] [Accepted: 12/10/2022] [Indexed: 12/29/2022]
Abstract
The spike (S) glycoprotein and nucleocapsid (N) proteins are the crucial pathogenic proteins of the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS CoV-2) virus during its interaction with the host. Even FDA-approved drugs like dexamethasone and grazoprevir are not able to curb the viral progression inside the host and are reported with adverse effects on body metabolism. In this context, we aim to report corilagin a novel, potential dual inhibitor of S and N proteins from Terminalia chebula. The bioactive compounds of T. chebula were subjected to a series of computational investigations including molecular docking simulations, molecular dynamics (MD) simulations, binding free energy calculations, and PASS pharmacological analysis. The results obtained from these studies revealed that corilagin was highly interactive with the S (-8.9 kcal/mol) and N (-9.2 kcal/mol) proteins, thereby showing dual inhibition activity. It was also found to be stable enough to induce biological activity inside the inhibitor binding pocket of the target enzymes throughout the dynamics simulation run for 100 ns. This is also confirmed by the changes in the protein conformations, evaluated using free energy landscapes. Outcomes from this investigation identify corilagin as the lead potential dual inhibitor of S and N proteins of SARS-CoV-2, which could be taken for biological studies in near future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sushma Pradeep
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education & Research, Mysuru, Karnataka, India
| | - Shashank M Patil
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education & Research, Mysuru, Karnataka, India
| | - Chandan Dharmashekara
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education & Research, Mysuru, Karnataka, India
| | - Anisha Jain
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education & Research, Mysuru, Karnataka, India
| | - Ramith Ramu
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education & Research, Mysuru, Karnataka, India
| | | | - Subhankar P Mandal
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru, Karnataka, India
| | - Pruthvish Reddy
- Department of Biotechnology, Acharya Institute of Technology, Bengaluru, Karnataka, India
| | - Chandrashekar Srinivasa
- Department of Studies in Biotechnology, Davangere University, Shivagangotri, Karnataka, India
| | - Sharanagouda S Patil
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Bengaluru, Karnataka, India
| | | | - Juan Frau
- Departament de Qúımica, Universitat de les Illes Balears, Palma de Malllorca, Spain
| | - Norma Flores-Holgúın
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energ'ıa, Centro de Investigación en Materiales Avanzados, Chihuahua, Chih, México
| | - Chandan Shivamallu
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education & Research, Mysuru, Karnataka, India
| | - Shiva Prasad Kollur
- School of Physical Sciences, Amrita Vishwa Vidyapeetham, Mysuru Campus, Mysuru, Karnataka, India
| | - Daniel Glossman-Mitnik
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energ'ıa, Centro de Investigación en Materiales Avanzados, Chihuahua, Chih, México
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Kokila NR, Mahesh B, Ramu R, Mruthunjaya K, Bettadaiah BK, Madhyastha H. Inhibitory effect of gallic acid from Thunbergia mysorensis against α-glucosidase, α-amylase, aldose reductase and their interaction: Inhibition kinetics and molecular simulations. J Biomol Struct Dyn 2023; 41:10642-10658. [PMID: 36533383 DOI: 10.1080/07391102.2022.2156923] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 12/04/2022] [Indexed: 12/23/2022]
Abstract
In this exploration, we assessed the antihyperglycaemic properties of methanol extract of flowers of Thunbergia mysorensis (MeT) against α-glucosidase, α-amylase and aldose reductase enzymes for the effective management of postprandial hyperglycemia. Hyperglycemia occurs when the body lacks enough insulin or is unable to correctly utilize it. MeT inhibited both the carbohydrate digestive enzymes (α-glucosidase and α-amylase) and aldose reductase, which are vital for the therapeutic control of postprandial hyperglycaemia. MeT was also found to have significant antioxidant activity. Using several spectroscopic approaches, the primary active component found in MeT was identified as gallic acid. With low Ki values, gallic acid significantly inhibited α-glucosidase (30.86 µg/mL) and α-amylase (6.50 µg/mL). Also, MeT and gallic acid both inhibited aldose reductase effectively, corresponding to an IC50 value of 3.31 and 3.05 µg/mL. Our findings imply that the presence of polyphenol compounds (identified via HPLC analysis) is more likely to be responsible for the antihyperglycaemic role exhibited by MeT via the inhibition of α-glucosidase and the polyol pathway. Further, gallic acid interacted with the key residues of the active sites of α-glucosidase (-6.4 kcal/mol), α-amylase (-5.8 kcal/mol) and aldose reductase (-5.8 kcal/mol) as observed in the protein-ligand docking. It was also predicted that gallic acid was stable inside the binding pockets of the target enzymes during molecular dynamics simulation. Overall, gallic acid derived from MeT via bioassay-guided isolation emerges as a natural antidiabetic drug and can be taken into in vivo and clinical studies shortly.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- N R Kokila
- Department of Chemistry, JSS Academy of Technical Education,(Affiliated to Visvesvaraya Technological University, Belagavi), Bengaluru, India
| | - B Mahesh
- Department of Chemistry, JSS Academy of Technical Education,(Affiliated to Visvesvaraya Technological University, Belagavi), Bengaluru, India
| | - Ramith Ramu
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, India
| | - K Mruthunjaya
- Department of Pharmacognosy, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Mysuru, India
| | - B K Bettadaiah
- Spices and Flavour Science Department, CSIR-Central Food Technological Research Institute, Mysuru, India
| | - Harishkumar Madhyastha
- Department of Cardiovascular Physiology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
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11
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Roopashree B, Mahesh B, Ramu R, Rekha ND, Manjula SN, Preethi G, Gayathri V. An insight into the cytotoxic, antimicrobial, antioxidant, and biocontrol perspective of novel Iron(III) complexes of substituted benzimidazoles: Inhibition kinetics and molecular simulations. J Biomol Struct Dyn 2023:1-17. [PMID: 37794762 DOI: 10.1080/07391102.2023.2263569] [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: 05/15/2023] [Accepted: 09/17/2023] [Indexed: 10/06/2023]
Abstract
Mononuclear complexes [FeCl3L2(OH2)] (L = L1, L2) were designed and synthesized by combining FeCl3 with 2-(3'-Aminophenylbenzimidazole) (L1) and 2-[(3'-N-Salicylidinephenyl)benzimidazole] (L2) and were characterized by physico-analytical strategies. The redox properties of the complexes were disclosed by the cyclic voltammetric method. Further, the interactions of complexes with proteins were studied by performing molecular docking engaging protein models of common cancer therapeutic targets to foresee their affinity to bind to these proteins. The complexes evidenced better protein-ligand docking (-8.4 and -9.0 kcal mol-1) and higher binding energies than their ligands. However, the L1 complex displayed improved binding free energy (-33.576 ± 1.01 kcal mol-1) compared to the other complexes and individual ligands. These compounds were screened for in vitro cytotoxic assays against triple-negative breast cancer cell lines (MDA-MB-468 cells), anti-inflammatory, antimicrobial, and antioxidant properties. The in vitro study complemented the in silico assay; therefore, these compounds may be a viable choice for expanding anticancer therapy. Additionally, the L2 showed better biocontrol activity owing to the enhanced growth of Trichoderma and inhibited the growth of Fusarium oxysporum.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- B Roopashree
- Department of Chemistry, JSS Academy of Technical Education (Affiliated to Visvesvaraya Technological University, Belagavi), Bengaluru, India
| | - B Mahesh
- Department of Chemistry, JSS Academy of Technical Education (Affiliated to Visvesvaraya Technological University, Belagavi), Bengaluru, India
| | - Ramith Ramu
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, India
| | - N D Rekha
- Department of Bio-Technology, JSS College of Arts, Commerce and Science (Autonomous), Mysuru, India
| | - S N Manjula
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Mysuru, India
| | - G Preethi
- Department of Chemistry, JSS Academy of Technical Education (Affiliated to Visvesvaraya Technological University, Belagavi), Bengaluru, India
| | - V Gayathri
- Department of Studies in Chemistry, Central College Campus, Bangalore City University, Bengaluru, India
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12
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Akash S, Abdelkrim G, Bayil I, Hosen ME, Mukerjee N, Shater AF, Saleh FM, Albadrani GM, Al‐Ghadi MQ, Abdel‐Daim MM, Tok TT. Antimalarial drug discovery against malaria parasites through haplopine modification: An advanced computational approach. J Cell Mol Med 2023; 27:3168-3188. [PMID: 37724615 PMCID: PMC10568677 DOI: 10.1111/jcmm.17940] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/20/2023] [Accepted: 08/24/2023] [Indexed: 09/21/2023] Open
Abstract
The widespread emergence of antimalarial drug resistance has created a major threat to public health. Malaria is a life-threatening infectious disease caused by Plasmodium spp., which includes Apicoplast DNA polymerase and Plasmodium falciparum cysteine protease falcipain-2. These components play a critical role in their life cycle and metabolic pathway, and are involved in the breakdown of erythrocyte hemoglobin in the host, making them promising targets for anti-malarial drug design. Our current study has been designed to explore the potential inhibitors from haplopine derivatives against these two targets using an in silico approach. A total of nine haplopine derivatives were used to perform molecular docking, and the results revealed that Ligands 03 and 05 showed strong binding affinity compared to the control compound atovaquone. Furthermore, these ligand-protein complexes underwent molecular dynamics simulations, and the results demonstrated that the complexes maintained strong stability in terms of RMSD (root mean square deviation), RMSF (root mean square fluctuation), and Rg (radius of gyration) over a 100 ns simulation period. Additionally, PCA (principal component analysis) analysis and the dynamic cross-correlation matrix showed positive outcomes for the protein-ligand complexes. Moreover, the compounds exhibited no violations of the Lipinski rule, and ADMET (absorption, distribution, metabolism, excretion, and toxicity) predictions yielded positive results without indicating any toxicity. Finally, density functional theory (DFT) and molecular electrostatic potential calculations were conducted, revealing that the mentioned derivatives exhibited better stability and outstanding performance. Overall, this computational approach suggests that these haplopine derivatives could serve as a potential source for developing new, effective antimalarial drugs to combat malaria. However, further in vitro or in vivo studies might be conducted to determine their actual effectiveness.
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Affiliation(s)
- Shopnil Akash
- Department of PharmacyFaculty of Allied Health Sciences, Daffodil International, UniversityDhakaBangladesh
| | - Guendouzi Abdelkrim
- Laboratory of Chemistry, Synthesis, Properties and Applications. (LCSPA)University of SaidaSaïdaAlgeria
| | - Imren Bayil
- Department of Bioinformatics and computational biologyGaziantep UniversityGaziantepTurkey
| | - Md. Eram Hosen
- Professor Joarder DNA and Chromosome Research Laboratory, Department of Genetic Engineering and BiotechnologyUniversity of RajshahiRajshahiBangladesh
| | - Nobendu Mukerjee
- Department of MicrobiologyWest Bengal State UniversityKolkataIndia
- Department of Health SciencesNovel Global Community Educational FoundationHebershamAustralia
| | - Abdullah F. Shater
- Department of Medical Laboratory Technology, Faculty of Applied Medical SciencesUniversity of TabukTabukSaudi Arabia
| | - Fayez M. Saleh
- Department of Medical Microbiology, Faculty of MedicineUniversity of TabukTabukSaudi Arabia
| | - Ghadeer M. Albadrani
- Department of Biology, College of SciencePrincess Nourah bint Abdulrahman UniversityRiyadhSaudi Arabia
| | - Muath Q. Al‐Ghadi
- Department of Zoology, College of ScienceKing Saud UniversityRiyadhSaudi Arabia
| | - Mohamed M. Abdel‐Daim
- Department of Pharmaceutical Sciences, Pharmacy ProgramBatterjee Medical CollegeJeddahSaudi Arabia
- Pharmacology Department, Faculty of Veterinary MedicineSuez Canal UniversityIsmailiaEgypt
| | - Tuğba Taşkin Tok
- Department of Bioinformatics and computational biologyGaziantep UniversityGaziantepTurkey
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13
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Dave B, Shah KC, Chorawala MR, Shah N, Patel P, Patel S, Shah P. Molnupiravir: an antiviral drug against COVID-19. Arch Virol 2023; 168:252. [PMID: 37710056 DOI: 10.1007/s00705-023-05881-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 05/28/2023] [Indexed: 09/16/2023]
Abstract
SARS-CoV-2, the virus responsible for COVID-19, has caused numerous deaths worldwide and poses significant challenges. Researchers have recently studied a new antiviral drug called molnupiravir for treating COVID-19. This review examines the causes and immunopathogenesis of COVID-19, as well as the role of molnupiravir in its treatment. Molnupiravir is a prodrug of β-D-N4-hydroxyctytidine (NHC) and has demonstrated activity against various viruses, including MERS-CoV, SARS-CoV, SARS-CoV-2, and influenza virus. The active form of molnupiravir, NHC triphosphate, acts as a nucleoside analog that disrupts viral replication by causing mutations in the viral RNA, thereby inhibiting viral growth. This review summarizes the results of multiple clinical trials that have evaluated the effectiveness of molnupiravir against SARS-CoV-2 and its variants. Animal studies have also shown that molnupiravir significantly reduces the viral load and prevents transmission to other animals. Overall, molnupiravir has demonstrated strong efficacy and reasonable safety, reducing hospitalization rates by nearly 50% among COVID-19-positive individuals at risk of complications. Patients in clinical settings have tolerated molnupiravir well and experienced positive outcomes, such as clearance of viral RNA, decreased viral load, and reduced hospitalization rates. Additionally, compared to a placebo, molnupiravir has been associated with lower mortality rates. Therefore, molnupiravir can be a beneficial drug to treat patients suffering from SARS-CoV-2, and further studies can provide more information about its safety and efficacy.
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Affiliation(s)
- Bhavarth Dave
- Department of Pharmacology and Pharmacy Practice, L. M. College of Pharmacy, Opp. Gujarat University, Navrangpura, Ahmedabad, Gujarat, 380 009, India
| | - Kashvi C Shah
- Department of Pharmacology and Pharmacy Practice, L. M. College of Pharmacy, Opp. Gujarat University, Navrangpura, Ahmedabad, Gujarat, 380 009, India
| | - Mehul R Chorawala
- Department of Pharmacology and Pharmacy Practice, L. M. College of Pharmacy, Opp. Gujarat University, Navrangpura, Ahmedabad, Gujarat, 380 009, India.
| | - Nirav Shah
- Department of Pharmaceutics, SAL Institute of Pharmacy, Sola, Ahmedabad, Gujarat, 380015, India
| | - Pranjal Patel
- Department of Pharmaceutics, SAL Institute of Pharmacy, Sola, Ahmedabad, Gujarat, 380015, India
| | - Suzan Patel
- Department of Pharmaceutics, SAL Institute of Pharmacy, Sola, Ahmedabad, Gujarat, 380015, India
| | - Palak Shah
- Department of Pharmacology and Pharmacy Practice, K. B. Institute of Pharmaceutical Education and Research, Gh-6, Sector-23, Gandhinagar, Gujarat, 382023, India
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14
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Akash S, Hosen ME, Mahmood S, Supti SJ, Kumer A, Sultana S, Jannat S, Bayıl I, Nafidi HA, Jardan YAB, Mekonnen AB, Bourhia M. Anti-parasitic drug discovery against Babesia microti by natural compounds: an extensive computational drug design approach. Front Cell Infect Microbiol 2023; 13:1222913. [PMID: 37662005 PMCID: PMC10469490 DOI: 10.3389/fcimb.2023.1222913] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 06/20/2023] [Indexed: 09/05/2023] Open
Abstract
Tick-borne Babesiosis is a parasitic infection caused by Babesia microti that can infect both animals and humans and may spread by tick, blood transfusions, and organ transplantation. The current therapeutic options for B. microti are limited, and drug resistance is a concern. This study proposes using computational drug design approaches to find and design an effective drug against B. microti. The study investigated the potentiality of nine natural compounds against the pathogenic human B. microti parasite and identified Vasicinone and Evodiamine as the most promising drugs. The ligand structures were optimized using density functional theory, molecular docking, molecular dynamics simulations, quantum mechanics such as HOMO-LUMO, drug-likeness and theoretical absorption, distribution, metabolism, excretion, and toxicity (ADMET), and pharmacokinetics characteristics performed. The results showed that Vasicinone (-8.6 kcal/mol and -7.8 kcal/mol) and Evodiamine (-8.7 kcal/mol and -8.5 kcal/mol) had the highest binding energy and anti-parasitic activity against B. microti lactate dehydrogenase and B. microti lactate dehydrogenase apo form. The strongest binding energy was reported by Vasicinone and Evodiamine; the compounds were evaluated through molecular dynamics simulation at 100 ns, and their stability when they form complexes with the targeted receptors was determined. Finally, the pkCSM web server is employed to predict the ADMET qualities of specific molecules, which can help prevent negative effects that arise from taking the treatment. The SwissADME web server is used to assess the Lipinski rule of five and drug-likeness properties including topological polar surface area and bioavailability. The Lipinski rule is used to estimate significant drug-likeness. The theoretical pharmacokinetics analysis and drug-likeness of the selected compounds are confirmed to be accepted by the Lipinski rule and have better ADMET features. Thus, to confirm their experimental value, these mentioned molecules should be suggested to carry out in wet lab, pre-clinical, and clinical levels.
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Affiliation(s)
- Shopnil Akash
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International, University, Dhaka, Bangladesh
| | - Md. Eram Hosen
- Professor Joarder DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Sajjat Mahmood
- Department of Microbiology, Jagannath University, Dhaka, Bangladesh
| | - Sumaiya Jahan Supti
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Ajoy Kumer
- Laboratory of Computational Research for Drug Design and Material Science, Department of Chemistry, European University of Bangladesh, Dhaka, Bangladesh
| | - Shamima Sultana
- Department of Pharmaceutical Sciences, School of Health and Life Sciences. North South University, Dhaka, Bangladesh
| | - Sultana Jannat
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, Bangladesh
| | - Imren Bayıl
- Department of Bioinformatics and Computational Biology, Gaziantep University, Gaziantep, Türkiye
| | - Hiba-Allah Nafidi
- Department of Food Science, Faculty of Agricultural and Food Sciences, Laval University, Quebec, QC, Canada
| | - Yousef A. Bin Jardan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | | | - Mohammed Bourhia
- Department of Chemistry and Biochemistry, Faculty of Medicine and Pharmacy, Ibn Zohr University, Laayoune, Morocco
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15
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Sreepathi N, Kumari VBC, Huligere SS, Al-Odayni AB, Lasehinde V, Jayanthi MK, Ramu R. Screening for potential novel probiotic Levilactobacillus brevis RAMULAB52 with antihyperglycemic property from fermented Carica papaya L. Front Microbiol 2023; 14:1168102. [PMID: 37408641 PMCID: PMC10318367 DOI: 10.3389/fmicb.2023.1168102] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/25/2023] [Indexed: 07/07/2023] Open
Abstract
Probiotics are live microorganisms with various health benefits when consumed in appropriate amounts. Fermented foods are a rich source of these beneficial organisms. This study aimed to investigate the probiotic potential of lactic acid bacteria (LAB) isolated from fermented papaya (Carica papaya L.) through in vitro methods. The LAB strains were thoroughly characterized, considering their morphological, physiological, fermentative, biochemical, and molecular properties. The LAB strain's adherence and resistance to gastrointestinal conditions, as well as its antibacterial and antioxidant capabilities, were examined. Moreover, the strains were tested for susceptibility against specific antibiotics, and safety evaluations encompassed the hemolytic assay and DNase activity. The supernatant of the LAB isolate underwent organic acid profiling (LCMS). The primary objective of this study was to assess the inhibitory activity of α-amylase and α-glucosidase enzymes, both in vitro and in silico. Gram-positive strains that were catalase-negative and carbohydrate fermenting were selected for further analysis. The LAB isolate exhibited resistance to acid bile (0.3% and 1%), phenol (0.1% and 0.4%), and simulated gastrointestinal juice (pH 3-8). It demonstrated potent antibacterial and antioxidant abilities and resistance to kanamycin, vancomycin, and methicillin. The LAB strain showed autoaggregation (83%) and adhesion to chicken crop epithelial cells, buccal epithelial cells, and HT-29 cells. Safety assessments indicated no evidence of hemolysis or DNA degradation, confirming the safety of the LAB isolates. The isolate's identity was confirmed using the 16S rRNA sequence. The LAB strain Levilactobacillus brevis RAMULAB52, derived from fermented papaya, exhibited promising probiotic properties. Moreover, the isolate demonstrated significant inhibition of α-amylase (86.97%) and α-glucosidase (75.87%) enzymes. In silico studies uncovered that hydroxycitric acid, one of the organic acids derived from the isolate, interacted with crucial amino acid residues of the target enzymes. Specifically, hydroxycitric acid formed hydrogen bonds with key amino acid residues, such as GLU233 and ASP197 in α-amylase, and ASN241, ARG312, GLU304, SER308, HIS279, PRO309, and PHE311 in α-glucosidase. In conclusion, Levilactobacillus brevis RAMULAB52, isolated from fermented papaya, possesses promising probiotic properties and exhibits potential as an effective remedy for diabetes. Its resistance to gastrointestinal conditions, antibacterial and antioxidant abilities, adhesion to different cell types, and significant inhibition of target enzymes make it a valuable candidate for further research and potential application in the field of probiotics and diabetes management.
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Affiliation(s)
- Navya Sreepathi
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
- Department of Pharmacology, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - V. B. Chandana Kumari
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Sujay S. Huligere
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Abdel-Basit Al-Odayni
- Department of Restorative Dental Science, College of Dentistry, King Saud University, Riyadh, Saudi Arabia
| | - Victor Lasehinde
- Department of Biology, Washington University, St. Louis, MO, United States
| | - M. K. Jayanthi
- Department of Pharmacology, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Ramith Ramu
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
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16
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Martiz RM, Kumari V. B. C, Huligere SS, Khan MS, Alafaleq NO, Ahmad S, Akhter F, Sreepathi N, P. A, Ramu R. Inhibition of carbohydrate hydrolyzing enzymes by a potential probiotic Levilactobacillus brevis RAMULAB49 isolated from fermented Ananas comosus. Front Microbiol 2023; 14:1190105. [PMID: 37389344 PMCID: PMC10303921 DOI: 10.3389/fmicb.2023.1190105] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/15/2023] [Indexed: 07/01/2023] Open
Abstract
The research aimed to explore the potential probiotic characteristics of Levilactobacillus brevis RAMULAB49, a strain of lactic acid bacteria (LAB) isolated from fermented pineapple, specifically focusing on its antidiabetic effects. The importance of probiotics in maintaining a balanced gut microbiota and supporting human physiology and metabolism motivated this research. All collected isolates underwent microscopic and biochemical screenings, and those exhibiting Gram-positive characteristics, negative catalase activity, phenol tolerance, gastrointestinal conditions, and adhesion capabilities were selected. Antibiotic susceptibility was assessed, along with safety evaluations encompassing hemolytic and DNase enzyme activity tests. The isolate's antioxidant activity and its ability to inhibit carbohydrate hydrolyzing enzymes were examined. Additionally, organic acid profiling (LC-MS) and in silico studies were conducted on the tested extracts. Levilactobacillus brevis RAMULAB49 demonstrated desired characteristics such as Gram-positive, negative catalase activity, phenol tolerance, gastrointestinal conditions, hydrophobicity (65.71%), and autoaggregation (77.76%). Coaggregation activity against Micrococcus luteus, Pseudomonas aeruginosa, and Salmonella enterica serovar Typhimurium was observed. Molecular characterization revealed significant antioxidant activity in Levilactobacillus brevis RAMULAB49, with ABTS and DPPH inhibition rates of 74.85% and 60.51%, respectively, at a bacterial cell concentration of 109 CFU/mL. The cell-free supernatant exhibited substantial inhibition of α-amylase (56.19%) and α-glucosidase (55.69%) in vitro. In silico studies supported these findings, highlighting the inhibitory effects of specific organic acids such as citric acid, hydroxycitric acid, and malic acid, which displayed higher Pa values compared to other compounds. These outcomes underscore the promising antidiabetic potential of Levilactobacillus brevis RAMULAB49, isolated from fermented pineapple. Its probiotic properties, including antimicrobial activity, autoaggregation, and gastrointestinal conditions, contribute to its potential therapeutic application. The inhibitory effects on α-amylase and α-glucosidase activities further support its anti-diabetic properties. In silico analysis identified specific organic acids that may contribute to the observed antidiabetic effects. Levilactobacillus brevis RAMULAB49, as a probiotic isolate derived from fermented pineapple, holds promise as an agent for managing diabetes. Further investigations should focus on evaluating its efficacy and safety in vivo to consider its potential therapeutic application in diabetes management.
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Affiliation(s)
- Reshma Mary Martiz
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
- Department of Microbiology, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Chandana Kumari V. B.
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Sujay S. Huligere
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Mohd Shahnawaz Khan
- Department of Biochemistry, College of Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Nouf Omar Alafaleq
- Department of Biochemistry, College of Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Saheem Ahmad
- Department of Biosciences, Integral University, Lucknow, India
| | - Firoz Akhter
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, United States
| | - Navya Sreepathi
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Ashwini P.
- Department of Microbiology, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Ramith Ramu
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
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17
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V. H. P, Kuruburu MG, M. K. J, N. AS, Taha Babakr A, Sreenivasan R, Ramu R, Madhunapantula SV. Bioactive profiling and evaluation of anti-proliferative and anti-cancerous properties of Shivagutika, an Indian polyherbal formulation synchronizing in vitro and in silico approaches. Front Chem 2023; 11:1195209. [PMID: 37265589 PMCID: PMC10230648 DOI: 10.3389/fchem.2023.1195209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 04/25/2023] [Indexed: 06/03/2023] Open
Abstract
Shivagutika is a polyherbal formulation mentioned in Ayurveda, the oldest system of medicine. The aim of this study was to investigate the anti-breast cancer potential of DCM extract of Shivagutika using MCF-7, MDA-MB-231, and MDA-MB-468. Primarily, various extracts of Shivagutika were prepared and subjected to primary in vitro analysis-total protein, phenolic acid content, and flavonoid content. DCM extract among all the extracts showed the promising results hence, it was subjected to LC-MS/MS analysis to identify the phytochemicals. The same extract was subjected to anti-proliferation assay and anti-cancer assay. It inhibited all the 3 cell lines and increased the activity of Caspase 3, pro-apoptotic protein. Further, to find the potent molecule(s) in silico analysis (molecular docking and molecular dynamics simulation studies) was performed. Sciadopitysin was identified as a potent molecule among all phytochemicals as it interacted with Caspase 3 with a binding energy of -7.2 kcal/mol. MD simulation studies also revealed that Sciadopitysin was stable inside the binding pocket of Caspase 3 by interacting with the amino acids in the catalytic site thereby activating the Caspase 3 levels. By all the above results, Shivagutika could be used as a potent anti-breast cancer agent (specifically DCM extract of Shivagutika) which could decrease the cases of breast cancer in future.
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Affiliation(s)
- Pushpa V. H.
- Department of Pharmacology, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Mahadevaswamy G. Kuruburu
- Center of Excellence in Molecular Biology and Regenerative Medicine (A DST-FIST Supported Center), Department of Biochemistry (A DST-FIST Supported Department), JSS Medical College, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Jayanthi M. K.
- Department of Pharmacology, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Akshaya Simha N.
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Abdullatif Taha Babakr
- Department of Medical Biochemistry, College of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | | | - Ramith Ramu
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - SubbaRao V. Madhunapantula
- Center of Excellence in Molecular Biology and Regenerative Medicine (A DST-FIST Supported Center), Department of Biochemistry (A DST-FIST Supported Department), JSS Medical College, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
- Special Interest Group in Cancer Biology and Cancer Stem Cells (SIG-CBCSC), JSS Medical College, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
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18
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Kumari V B C, Huligere SS, Alotaibi G, Al Mouslem AK, Bahauddin AA, Shivanandappa TB, Ramu R. Antidiabetic Activity of Potential Probiotics Limosilactobacillus spp., Levilactobacillus spp., and Lacticaseibacillus spp. Isolated from Fermented Sugarcane Juice: A Comprehensive In Vitro and In Silico Study. Nutrients 2023; 15:nu15081882. [PMID: 37111101 PMCID: PMC10144524 DOI: 10.3390/nu15081882] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
Probiotics are regarded as a potential source of functional foods for improving the microbiota in human gut. When consumed, these bacteria can control the metabolism of biomolecules, which has numerous positive effects on health. Our objective was to identify a probiotic putative Lactobacillus spp. from fermented sugarcane juice that can prevent α-glucosidase and α-amylase from hydrolyzing carbohydrates. Isolates from fermented sugarcane juice were subjected to biochemical, molecular characterization (16S rRNA) and assessed for probiotic traits. Cell-free supernatant (CS) and extract (CE) and also intact cells (IC) were examined for the inhibitory effect on α-glucosidase and α-amylase. CS of the strain showed the highest inhibition and was subjected to a liquid chromatography-mass spectrometry (LCMS) analysis to determine the organic acid profile. The in silico approach was employed to assess organic acid stability and comprehend enzyme inhibitors' impact. Nine isolates were retained for further investigation based on the preliminary biochemical evaluation. Limosilactobacillus spp., Levilactobacillus spp., and Lacticaseibacillus spp. were identified based on similarity > 95% in homology search (NCBI database). The strains had a higher survival rate (>98%) than gastric and intestinal fluids, also a high capacity for adhesion (hydrophobicity > 56%; aggregation > 80%; HT-29 cells > 54%; buccal epithelial cells > 54%). The hemolytic assay indicated that the isolates could be considered safe. The isolates' derivatives inhibited enzymes to varying degrees, with α-glucosidase inhibition ranging from 21 to 85% and α-amylase inhibition from 18 to 75%, respectively. The CS of RAMULAB54 was profiled for organic acid that showed the abundance of hydroxycitric acid, citric acid, and lactic acid indicating their role in the observed inhibitory effects. The in silico approach has led us to understand that hydroxycitric acid has the ability to inhibit both the enzymes (α-glucosidase and α-amylase) effectively. Inhibiting these enzymes helps moderate postprandial hyperglycemia and regulates blood glucose levels. Due to their promising antidiabetic potential, these isolates can be used to enhance intestinal health.
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Affiliation(s)
- Chandana Kumari V B
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru 570015, Karnataka, India
| | - Sujay S Huligere
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru 570015, Karnataka, India
| | - Ghallab Alotaibi
- Department of Pharmaceutical Sciences, College of Pharmacy, Shaqra University, Al-Dawadmi Campus, Shaqra 11961, Saudi Arabia
| | - Abdulaziz K Al Mouslem
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al Ahsa 31982, Saudi Arabia
| | - Ammar Abdulraheem Bahauddin
- Department of Pharmacology and Toxicology, College of Pharmacy, Taibah University, Madinah 42535, Saudi Arabia
| | | | - Ramith Ramu
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru 570015, Karnataka, India
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Kokila NR, Mahesh B, Ramu R, Roopashree B, Mruthunjaya K. α-Amylase inhibitory potential of Thunbergia mysorensis leaves extract and bioactive compounds by in vitro and computational approach. J Biomol Struct Dyn 2023; 41:14887-14903. [PMID: 36927385 DOI: 10.1080/07391102.2023.2190408] [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: 12/29/2022] [Accepted: 02/18/2023] [Indexed: 03/18/2023]
Abstract
In this study, we aim to evaluate the anti-diabetic potential of Thunbergia mysorensis leaves methanolic extract (MeL) using inhibitory assays for α-glucosidase (AG), α-amylase (AM) (carbohydrate digestive enzymes) and aldose reductase (AR) (an enzyme involved in the polyol pathway responsible for glycation). In addition to antidiabetic studies, antioxidant studies were also performed due to the fact that reactive oxygen species (ROS) are produced by various pathways under diabetic conditions. Hyperglycemia induces ROS by activating the glycation reaction and the electron transport chain in mitochondria. The MeL effectively inhibited the enzymes (AG IC50: 27.86 ± 1.0, AM IC50: 12.00 ± 0.0, AR IC50: 4.50 ± 0.09 μg/mL) and showed effective radical ion scavenging activity during the antioxidant assay (DPPH EC50: 30.10 ± 0.75, ABTS EC50: 27.25 ± 1.00, Superoxide EC50: 35.00 ± 1.50 μg/mL). Using activity-guided repeated fractionation on a silica gel column chromatography, two compounds including 3,4-dimethoxy benzoic acid (DMBA) (101 mg) and 3,4-dimethoxy cinnamic acid (DMCA) (87 mg) with potent anti-diabetic activity were extracted from the MeL of T. mysorensis leaves. Both DMBA (IC50 AG: 27.00 ± 1.05, IC50 AM: 12.15 ± 0.10, IC50 AR: 4.86 ± 0.30 μg/mL) and DMCA (IC50 AG: 27.25 ± 0.98, IC50 AM: 12.50 ± 0.20, IC50 AR: 5.00 ± 1.00 μg/mL) were subjected for enzyme inhibition. Since both compounds significantly inhibited AM, enzyme kinetics for AM inhibition was performed. The compounds also showed effective antioxidant potential (DPPH EC50: 30.50 ± 0.99, ABTS EC50: 27.86 ± 0.16, Superoxide EC50: 36.10 ± 0.24 μg/mL), and DMCA (DPPH EC50: 31.00 ± 1.00, ABTS EC50: 28.00 ± 0.25, Superoxide EC50: 36.25 ± 0.37 μg/mL). Further, to elucidate the role of DMBA and DMCA in enzyme inhibition and stability at the molecular level, both compounds were subjected for in silico enzyme inhibitory studies using molecular docking simulation, molecular dynamics (MD) simulation, and binding free energy calculations. Compared to AR and AG, AM was the most significantly inhibited enzyme (DMBA: -6.6 and DMCA: -7.8 kcal/mol), and compounds combined with AM were subjected to MD simulation. Both compounds were stable in the binding pocket of AM till 100 ns and chiefly use Van der Waal's energy to bind. Compared to the controls, both DMBA and DMCA had a higher efficiency in the inhibition of target enzymes in vitro and in silico. The presence of DMBA and DMCA is more likely to be associated with the potential of MeL in antihyperglycemic activity. This bio-computational study indicates DMBA and DMCA as potential lead inhibitors of AM and could be used as effective anti-diabetic drugs in the near future.
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Affiliation(s)
- N R Kokila
- Department of Chemistry, JSS Academy of Technical Education (Affiliated to Visvesvaraya Technological University, Belagavi), Bengaluru, India
| | - B Mahesh
- Department of Chemistry, JSS Academy of Technical Education (Affiliated to Visvesvaraya Technological University, Belagavi), Bengaluru, India
| | - Ramith Ramu
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, India
| | - B Roopashree
- Department of Chemistry, JSS Academy of Technical Education (Affiliated to Visvesvaraya Technological University, Belagavi), Bengaluru, India
| | - K Mruthunjaya
- Department of Pharmacognosy, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Mysuru, India
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Liu Y. Integrative network pharmacology and in silico analyses identify the anti-omicron SARS-CoV-2 potential of eugenol. Heliyon 2023; 9:e13853. [PMID: 36845041 PMCID: PMC9937729 DOI: 10.1016/j.heliyon.2023.e13853] [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: 04/03/2022] [Revised: 02/06/2023] [Accepted: 02/13/2023] [Indexed: 02/19/2023] Open
Abstract
Eugenol as a natural product is the source of isoniazid, and purified eugenol is extensively used in the cosmetics industry and the productive processes of edible spices. Accumulating evidence suggested that eugenol exerted potent anti-microorganism and anti-inflammation effects. Application of eugenol effectively reduced the risk of atherosclerosis, arterial embolism, and Type 2 diabetes. A previous study confirmed that treatment with eugenol attenuated lung inflammation and improved heart functions in SARS-CoV-2 spike S1-intoxicated mice. In addition to the study, based on a series of public datasets, computational analyses were conducted to characterize the acting targets of eugenol and the functional roles of these targets in COVID-19. The binding capacities of eugenol to conservative sites of SARS-CoV-2 like RNA-dependent RNA polymerase (RdRp) and mutable site as spike (S) protein, were calculated by using molecular docking following the molecular dynamics simulation with RMSD, RMSF, and MM-GBSA methods. The results of network pharmacology indicated that six targets, including PLAT, HMOX1, NUP88, CTSL, ITGB1 andTMPRSS2 were eugenol-SARS-CoV-2 interacting proteins. The omics results of in-silico study further implicated that eugenol increased the expression of SCARB1, HMOX1 and GDF15, especially HMOX1, which were confirmed the potential interacting targets between eugenol and SARS-CoV-2 antigens. Enrichment analyses indicated that eugenol exerted extensive biological effects such as regulating immune infiltration of macrophage, lipid localization, monooxyenase activity, iron ion binding and PPAR signaling. The results of the integrated analysis of eugenol targets and immunotranscription profile of COVID-19 cases shows that eugenol also plays an important role in strengthen of immunologic functions and regulating cytokine signaling. As a complement to the integrated analysis, the results of molecular docking indicated the potential binding interactions between eugenol and four proteins relating to cytokine production/release and the function of T type lymphocytes, including human TLR-4, TCR, NF-κB, JNK and AP-1. Furthermore, results of molecular docking and molecular dynamics (100ns) simulations implicated that stimulated modification of eugenol to the SARS-CoV-2 Omicron Spike-ACE2 complex, especially for human ACE2, and the molecular interaction of eugenol to SARS-CoV-2 RdRp, were no less favorable than two positive controls, molnupiravir and nilotinib. Dynamics (200ns) simulations indicated that the binding capacities and stabilities of eugenol to finger subdomain of RdRp is no less than molnupiravir. However, the simulated binding capacity of eugenol to SARS-CoV-2 wild type RBD and Omicron mutant RBD were less than nilotinib. Eugenol was predicted to have more favor LD50 value and lower cytotoxicity than two positive controls, and eugenol can pass through the blood-brain barrier (BBB). In a brief, eugenol is helpful for attenuating systemic inflammation induced by SARS-CoV-2 infection, due to the direct interaction of eugenol to SARS-CoV-2 proteins and extensive bio-manipulation of pro-inflammatory factors. This study carefully suggests eugenol is a candidate compound of developing drugs and supplement agents against SARS-CoV-2 and its Omicron variants.
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Affiliation(s)
- Yang Liu
- Graduated Student of Harbin Medical University, Cardiology. Baojian Road105, Nangang Distinct, Harbin, Heilongjiang, China
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Patil SM, Phanindra B, Shirahatti PS, Martiz RM, Sajal H, Babakr AT, Ramu R. Computational approaches to define poncirin from Magnolia champaka leaves as a novel multi-target inhibitor of SARS-CoV-2. J Biomol Struct Dyn 2023; 41:13078-13097. [PMID: 36695109 DOI: 10.1080/07391102.2023.2171137] [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: 11/10/2022] [Accepted: 01/13/2023] [Indexed: 01/26/2023]
Abstract
Phytochemical-based drug discovery against the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been the focus of the current scenario. In this context, we aimed to perform the phytochemical profiling of Magnolia champaka, an evergreen tree from the Magnoliaceae family, in order to perform a virtual screening of its phytoconstituents against different biological targets of SARS-CoV-2. The phytochemicals identified from the ethanol extract of M. champaka leaves using liquid chromatography-mass spectroscopy (LC-MS) technique were screened against SARS-CoV-2 spike glycoprotein (PDB ID: 6M0J), main protease/Mpro (PDB ID: 6LU7), and papain-like protease/PLpro (PDB ID: 7CMD) through computational tools. The experimentation design included molecular docking simulation, molecular dynamics simulation, and binding free energy calculations. Through molecular docking simulation, we identified poncirin as a common potential inhibitor of all the above-mentioned target proteins. In addition, molecular dynamics simulations, binding free energy calculations, and PCA analysis also supported the outcomes of the virtual screening. By the virtue of all the in silico results obtained, poncirin could be taken for in vitro and in vivo studies in near future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shashank M Patil
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysore, Karnataka, India
| | - Bhaskar Phanindra
- Department of Pharmacology, JSS Medical College, JSS Academy of Higher Education and Research, Mysore, Karnataka, India
| | | | - Reshma Mary Martiz
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysore, Karnataka, India
| | - Harshit Sajal
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysore, Karnataka, India
| | - Abdullatif Taha Babakr
- Department of Medical Biochemistry - College of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Ramith Ramu
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysore, Karnataka, India
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22
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Maradesha T, Martiz RM, Patil SM, Prasad A, Babakr AT, Silina E, Stupin V, Achar RR, Ramu R. Integrated network pharmacology and molecular modeling approach for the discovery of novel potential MAPK3 inhibitors from whole green jackfruit flour targeting obesity-linked diabetes mellitus. PLoS One 2023; 18:e0280847. [PMID: 36716329 PMCID: PMC9886246 DOI: 10.1371/journal.pone.0280847] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/10/2023] [Indexed: 02/01/2023] Open
Abstract
The current study investigates the effectiveness of phytocompounds from the whole green jackfruit flour methanol extract (JME) against obesity-linked diabetes mellitus using integrated network pharmacology and molecular modeling approach. Through network pharmacology, druglikeness and pharmacokinetics, molecular docking simulations, GO analysis, molecular dynamics simulations, and binding free energy analyses, it aims to look into the mechanism of the JME phytocompounds in the amelioration of obesity-linked diabetes mellitus. There are 15 predicted genes corresponding to the 11 oral bioactive compounds of JME. The most important of these 15 genes was MAPK3. According to the network analysis, the insulin signaling pathway has been predicted to have the strongest affinity to MAPK3 protein, which was chosen as the target. With regard to the molecular docking simulation, the greatest notable binding affinity for MAPK3 was discovered to be caffeic acid (-8.0 kJ/mol), deoxysappanone B 7,3'-dimethyl ether acetate (DBDEA) (-8.2 kJ/mol), and syringic acid (-8.5 kJ/mol). All the compounds were found to be stable inside the inhibitor binding pocket of the enzyme during molecular dynamics simulation. During binding free energy calculation, all the compounds chiefly used Van der Waal's free energy to bind with the target protein (caffeic acid: 102.296 kJ/mol, DBDEA: -104.268 kJ/mol, syringic acid: -100.171 kJ/mol). Based on these findings, it may be inferred that the reported JME phytocompounds could be used for in vitro and in vivo research, with the goal of targeting MAPK3 inhibition for the treatment of obesity-linked diabetes mellitus.
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Affiliation(s)
- Tejaswini Maradesha
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Reshma Mary Martiz
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
- Department of Microbiology, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Shashank M. Patil
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Ashwini Prasad
- Department of Microbiology, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Abdullatif Taha Babakr
- Department of Medical Biochemistry, College of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Ekaterina Silina
- Institute of Biodesign and Modeling of Complex Systems, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Victor Stupin
- Department of Hospital Surgery 1, N.I. Pirogov Russian National Research Medical University (RNRMU), Moscow, Russia
| | - Raghu Ram Achar
- Division of Biochemistry, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Ramith Ramu
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
- * E-mail:
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23
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Shadakshari A, Suresha Kumara T, Kumar N, Jagadeep Chandra S, Anil Kumar K, Ramu R. Synthesis, Characterization, and biocomputational assessment of the novel 3-hydroxy-4-(phenyl(pyridin-2-ylamino) methyl)-2-naphthoic acid derivatives as potential dual inhibitors of α-glucosidase and α-amylase enzymes. RESULTS IN CHEMISTRY 2022. [DOI: 10.1016/j.rechem.2022.100745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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24
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V. H. P, M. K. J, H. R. R, Shivamurthy VKN, Patil SM, Shirahatti PS, Ramu R. New insights on the phytochemical intervention for the treatment of neuropsychiatric disorders using the leaves of Michelia champaca: an in vivo and in silico approach. PHARMACEUTICAL BIOLOGY 2022; 60:1656-1668. [PMID: 36052952 PMCID: PMC9448401 DOI: 10.1080/13880209.2022.2101669] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
CONTEXT Michelia champaca L. (Magnoliaceae) has been known since ancient times for its rich medicinal properties. OBJECTIVE The ethanol extract of Michelia champaca leaves (EEMC) was evaluated on depression and anxiety using in vivo and in silico studies. MATERIALS AND METHODS Swiss albino mice were divided into control, standard, 100 and 200 mg/kg b.w. EEMC groups and for drug administration using oral gavage. The antidepressant activity was evaluated using forced swim test (FST) and tail suspension test (TST) whereas the anxiolytic activity through elevated plus maze and light and dark tests. The in silico studies included molecular docking against human potassium channel KCSA-FAB and human serotonin transporter, and ADME/T analysis. RESULTS Open arm duration and entries were comparable between 200 mg/kg b.w. group (184.45 ± 1.00 s and 6.25 ± 1.11, respectively) and that of diazepam treated group (180.02 s ± 0.40 and 6.10 ± 0.05, respectively). Time spent in the light cubicle was higher (46.86 ± 0.03%), similar to that of diazepam (44.33 ± 0.64%), suggesting its potent anxiolytic activity. A delayed onset of immobility and lowered immobility time was seen at both the treatment doses (FST: 93.7 ± 1.70 and 89.1 ± 0.40 s; TST: 35.05 ± 2.75 and 38.50 ± 4.10 s) and the standard drug imipramine (FST: 72.7 ± 3.72 and TST: 30.01 ± 2.99 s), indicative of its antidepressant ability. In silico studies predicted doripenem to induce anxiolytic and antidepressant activity by inhibiting human potassium channel KCSA-FAB and human serotonin transporter proteins, respectively. CONCLUSIONS EEMC is a rich source of bioactive compounds with strong antidepressant and anxiolytic properties.
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Affiliation(s)
- Pushpa V. H.
- Department of Pharmacology, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru, India
- CONTACT Pushpa V. H. Department of Pharmacology, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru, Karnataka570015, India
| | - Jayanthi M. K.
- Department of Pharmacology, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru, India
| | - Rashmi H. R.
- Department of Pharmacology, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru, India
| | - Veeresh Kumar N. Shivamurthy
- Department of Neurology, Saint Francis Hospital and Medical Center, Trinity Health Of New England, Hartford, CT, USA
| | - Shashank M. Patil
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru, India
| | - Prithvi S. Shirahatti
- Department of Biotechnology, Teresian College, Mysuru, India
- St. Joseph's College for Women, Mysore, Karnataka, India
| | - Ramith Ramu
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru, India
- Ramith Ramu Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru, India
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Badiger AS, Jayadev K, Manu G, Raj R, Ammanagi A, Bajpe SN, Ramu R. Molecular docking and simulation analysis of the FimH protein with secondary metabolites from the Garcinia species. Bioinformation 2022; 18:76-81. [PMID: 36420433 PMCID: PMC9649499 DOI: 10.6026/97320630018076] [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: 11/14/2021] [Revised: 12/31/2021] [Accepted: 12/31/2021] [Indexed: 09/19/2023] Open
Abstract
It is of interest to document the molecular docking and simulation analysis of the FimH protein with 10 secondary metabolites from Garcinia species in the context of drug discovery for Urinary tract infections (UTIs). We report the optimal binding features of flavonoids with the FimH protein for further consideration in drug discovery.
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Affiliation(s)
- Abhijeeth S Badiger
- Department of Biotechnology, Sri Dharmasthala Manjunatheshwara College, Ujire - 574240, Karnataka, India
- Department of PG studies in Biotechnology, Alva's College, Moodbidri - 574227, Karnataka, India
| | - K Jayadev
- Department of PG studies in Biotechnology, Alva's College, Moodbidri - 574227, Karnataka, India
| | - G Manu
- Department of Pharmacology, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru - 570015, Karnataka, India
| | - Ranjith Raj
- Department of Pharmacology, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru - 570015, Karnataka, India
| | - Avinash Ammanagi
- Department of PG studies in Microbiology and Biotechnology, Karnataka University, Dharwad - 580003, Karnataka, India
| | - Shrisha Naik Bajpe
- Department of Biotechnology, Sri Dharmasthala Manjunatheshwara College, Ujire - 574240, Karnataka, India
| | - Ramith Ramu
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru-570015, Karnataka, India
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Mahnashi MH, El-Senduny FF, Alshahrani MA, Abou-Salim MA. Design, Synthesis, and Biological Evaluation of a Novel VEGFR-2 Inhibitor Based on a 1,2,5-Oxadiazole-2-Oxide Scaffold with MAPK Signaling Pathway Inhibition. Pharmaceuticals (Basel) 2022; 15:246. [PMID: 35215358 PMCID: PMC8880564 DOI: 10.3390/ph15020246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 12/04/2022] Open
Abstract
Over the past few decades, the development of broad-spectrum anticancer agents with anti-angiogenic activity has witnessed considerable progress. In this study, a new series of pyrazolo[3,4-d]pyrimidines based on a phenylfuroxan scaffold were designed, synthesized, and evaluated, in terms of their anticancer activities. NCI-60 cell one-dose screening revealed that compounds 12a-c and 14a had the best MGI%, among the tested compounds. The target fluorinated compound 12b, as the most active one, showed better anticancer activity compared to the reference drug sorafenib, with IC50 values of 11.5, 11.6, and 13 µM against the HepG-2, A2780CP, and MDA-MB-231 cell lines, respectively. Furthermore, compound 12b (IC50 = 0.092 µM) had VEGFR-2-inhibitory activity comparable to that of the standard inhibitor sorafenib (IC50 = 0.049 µM). Furthermore, the ability of compound 12b in modulating MAPK signaling pathways was investigated. It was found to decrease the level of total ERK and its phosphorylated form, as well as leading to the down-regulation of metalloproteinase MMP-9 and the over-expression of p21 and p27, thus leading to subG1 cell-cycle arrest and, thus, the induction of apoptosis. Additionally, compound 12b decreased the rate of wound healing in the absence of serum, in comparison to DMSO-treated cells, providing a significant impact on metastasis inhibition. The quantitative RT-PCR results for E-cadherin and N-cadherin showed lower expression of the neuronal N-cadherin and increased expression of epithelial E-cadherin, indicating the ability of 12b to suppress metastasis. Furthermore, 12b-treated HepG2 cells expressed a low level of anti-apoptotic BCL-2 and over-expressed proapoptotic Bax genes, respectively. Using the DAF-FM DA fluorescence probe, compound 12b produced NO intracellularly as efficiently as the reference drug JS-K. In silico molecular docking studies showed a structural similarity through an overlay of 12b with sorafenib. Interestingly, the drug-likeness properties of compound 12b met the expectations of Pfizer's rule for the design of new drug candidates. Therefore, this study presents a novel anticancer lead compound that is worthy of further investigation and activity improvement.
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Affiliation(s)
- Mater H. Mahnashi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Najran University, Najran 61441, Saudi Arabia;
| | - Fardous F. El-Senduny
- Chemistry Department, Faculty of Science, Mansoura University, Mansoura 35516, Egypt;
| | - Mohammed Abdulrahman Alshahrani
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia;
| | - Mahrous A. Abou-Salim
- Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Al-Azhar University, Assiut 71524, Egypt
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Prabhakaran S, Nivetha N, Patil SM, Mary Martiz R, Ramu R, Sreenivasa S, Velmathi S. One-pot three-component synthesis of novel phenyl-pyrano-thiazol-2-one derivatives and their anti-diabetic activity studies. RESULTS IN CHEMISTRY 2022. [DOI: 10.1016/j.rechem.2022.100439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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