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Wahid M, Saqib F, Abbas G, Shah S, Alshammari A, Albekairi TH, Ali A, Khurm M, Mubarak MS. Cardioprotective and hypotensive mechanistic insights of hydroethanolic extract of Cucumis melo L. kernels in isoprenaline-induced cardiotoxicity based on metabolomics and in silico electrophysiological models. Front Pharmacol 2024; 14:1277594. [PMID: 38348351 PMCID: PMC10859416 DOI: 10.3389/fphar.2023.1277594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 12/26/2023] [Indexed: 02/15/2024] Open
Abstract
Background: Cardiovascular diseases (CVD) continue to threaten health worldwide, and account for a significant portion of deaths and illnesses. In both developing and industrialized nations, they challenge their health systems. There are several traditional uses of Cucurbitaceae seeds in Pakistan, India, Iran, and China, including treating cardiovascular, neurological, and urogenital diseases. Methods: In the present work, integrated techniques of metabolomics profiling and computational cardiomyocyte stimulation were used to investigate possible mechanisms of C. melo in isoprenaline (ISO)-induced myocardial infarction. In vitro, vasoconstrictions, paired atria, and in vivo invasive blood pressure measurement models were performed to explore the mechanism of action of C. melo hydroethanolic seed extract (Cm-EtOH). Results: Results showed that Cm-EtOH demonstrates NO-based endothelium-derived relaxing factor (EDRF) vasorelaxant response, negative chronotropic and inotropic response in the atrium, and hypotensive effects in normotensive rats. Results also revealed that Cm-EtOH decreases cardiomyocyte hypertrophy and reverts the altered gene expressions, biochemical, and metabolites in ISO-induced myocardial infarction (MI) rats. The extract additionally reversed ISO-induced MI-induced oxidative stress, energy consumption, and amino acid metabolism. Moreover, C. melo seeds increased EDRF function, energy production, and antioxidant capacity to treat myocardial and vascular disorders. In computational cardiomyocyte simulation, gallic acid reduced action potential duration, upstroke velocity (dV/dtmax), and effective refractory period. Conclusion: This study highlights the therapeutic potential of C. melo seeds to treat cardiovascular diseases and provides mechanistic insight into its antihypertensive and cardioprotective activities.
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Affiliation(s)
- Muqeet Wahid
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan, Pakistan
| | - Fatima Saqib
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan, Pakistan
| | - Ghulam Abbas
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Government College University Faisalabad, Faisalabad, Pakistan
| | - Shahid Shah
- Department of Pharmacy Practice, Faculty of Pharmaceutical Sciences, Government College University Faisalabad, Faisalabad, Pakistan
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Thamer H. Albekairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Anam Ali
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan, Pakistan
| | - Muhammad Khurm
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
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Shah SA, Rana SL, Mohany M, Milošević M, Al-Rejaie SS, Farooq MA, Faisal MN, Aleem A. Fumaria indica (Hausskn.) Pugsley Hydromethanolic Extract: Bioactive Compounds Identification, Hypotensive Mechanism, and Cardioprotective Potential Exploration. ACS OMEGA 2024; 9:3642-3668. [PMID: 38284069 PMCID: PMC10809708 DOI: 10.1021/acsomega.3c07655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/26/2023] [Accepted: 12/11/2023] [Indexed: 01/30/2024]
Abstract
Fumaria indica (Hausskn.) Pugsley (FIP), a member of the Papaveraceae family, has a documented history of use in traditional medicine to treat cardiovascular ailments, particularly hypertension, and has shown substantial therapeutic efficacy among native cultures worldwide. However, the identification of bioactive compounds and the mechanism of hypotensive effect with the cardioprotective potential investigations are yet to be determined. The study aimed to identify bioactive compounds, explore the hypotensive mechanism and cardioprotective potential, and assess the safety of Fumaria indica (Hausskn.) Pugsley hydromethanolic extract (Fip.Cr). LC ESI-MS/MS analysis was performed to identify the bioactive compounds. In vitro experiments were conducted on isolated rat aorta and atria, and an in vivo invasive BP measurement model was used. Acute and subacute toxicities were assessed for 14 and 28 days, respectively. Isoproterenol (ISO) was used to develop the rats' myocardial infarction damage model. The mRNA levels of NLRP3 inflammasome and the abundance level of Firmicutes and Lactobacillus were measured by qRT-PCR. The hypotensive effect of FIP bioactive compounds was also investigated using in silico methods. Fip. Cr LC ESI-MS/MS analysis discovered 33 bioactive compounds, including alkaloids and flavonoids. In isolated rat aorta, Fip.Cr reversed contractions induced by K+ (80 mM), demonstrating a calcium entry-blocking function, and had a vasorelaxant impact on phenylephrine (PE) (1 μM)-induced contractions unaffected by L-NAME, ruling out endothelial NO participation. Fip.Cr caused negative chronotropic and inotropic effects in isolated rat atria unaffected by atropine pretreatment, eliminating cardiac muscarinic receptor involvement. Safety evaluation showed no major adverse effects. In vivo, invasive BP measurement demonstrated a hypotensive effect comparable to verapamil. Fip.Cr protected the rats from ISO-induced MI interventions significantly in biometrical and cardiac serum biochemical indicators and histological examinations by reducing inflammation via inhibiting NLRP3 inflammasome and elevating Firmicutes and Lactobacillus levels. The network pharmacology study revealed that the FIP hypotensive mechanism might involve MMP9, JAK2, HMOX1, NOS2, NOS3, TEK, SERPINE1, CCL2, and VEGFA. The molecular docking study revealed that FIP bioactive compounds docked better with CAC1C_ HUMAN than verapamil. These findings demonstrated that Fip.Cr's hypotensive mechanism may include calcium channel blocker activity. Fip.Cr ameliorated ISO-induced myocardial infarction in rats by attenuating inflammation, which might be via inhibiting NLRP3 inflammasome and may prove beneficial for treating MI.
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Affiliation(s)
- Syed Adil
Hussain Shah
- Department
of Pharmacology, Faculty of Pharmacy, Bahauddin
Zakariya University, Multan 60800, Pakistan
| | - Samia Latif Rana
- Department
of Pharmacology, Faculty of Pharmacy, Bahauddin
Zakariya University, Multan 60800, Pakistan
| | - Mohamed Mohany
- Department
of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 55760, Riyadh 11451, Saudi Arabia
| | - Marija Milošević
- Department
of Biology and Ecology, Faculty of Science, University of Kragujevac, 34000 Kragujevac, Serbia
| | - Salim S. Al-Rejaie
- Department
of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 55760, Riyadh 11451, Saudi Arabia
| | | | - Muhammad Naeem Faisal
- Institute
of Physiology and Pharmacology, University
of Agriculture, Faisalabad 60800, Pakistan
| | - Ambreen Aleem
- Department
of Pharmacology, Faculty of Pharmacy, Bahauddin
Zakariya University, Multan 60800, Pakistan
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N SD, Shivakumar, Kumar D U, Ghate SD, Dixit SR, Awasthi A, Revanasiddappa BC. Benzothiazole derivatives as p53-MDM2 inhibitors: in-silico design, ADMET predictions, molecular docking, MM-GBSA Assay, MD simulations studies. J Biomol Struct Dyn 2023:1-12. [PMID: 38111168 DOI: 10.1080/07391102.2023.2294836] [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: 07/04/2023] [Accepted: 12/09/2023] [Indexed: 12/20/2023]
Abstract
Breast cancer stands as the most prevalent malignancy among the female populace. One of the pivotal domains in the therapeutic landscape of breast cancer revolves around the precise targeting of the p53-MDM2 inhibitory pathway. The advent of p53-MDM2 inhibition in the context of developing treatments for breast cancer marks a significant stride. In the quest for enhancing the efficacy of p53-MDM2 inhibition against breast cancer, a new series of benzothiazole compounds (B1-B30) was designed through in-silico methodologies in the present work. Using Schrodinger Maestro, the compounds underwent molecular docking assessments against the p53-MDM2 target (PDB: 4OGT). Compared to reference compounds, B25 and B12 exhibited notably elevated glide scores. Extensive in-silico studies, including ADMET and toxicity evaluations, were performed to predict pharmacokinetics, drug likeness, and toxicity. All compounds adhered to Lipinski criteria, signifying favorable oral drug properties. The MM-GBSA analysis indicated consistent binding free energies. Molecular dynamics simulations for B25 over 200 ns assessed complex stability and interactions. In summary, these compounds exhibit potential for future cancer therapy medication development.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shridhar Deshpande N
- Department of Pharmaceutical Chemistry, NGSM Institute of Pharmaceutical Sciences (NGSMIPS), Nitte (Deemed to be University), Mangalore, Karnataka, India
| | - Shivakumar
- Department of Chemistry, National Institute of Technology Karnataka, Mangalore, Karnataka, India
| | - Udaya Kumar D
- Department of Chemistry, National Institute of Technology Karnataka, Mangalore, Karnataka, India
| | - Sudeep D Ghate
- Center for Bioinformatics, Nitte (Deemed to be University), Deralakatte, Karnataka, India
| | - Sheshagiri R Dixit
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Karnataka, India
| | - Abhimanyu Awasthi
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Karnataka, India
| | - B C Revanasiddappa
- Department of Pharmaceutical Chemistry, NGSM Institute of Pharmaceutical Sciences (NGSMIPS), Nitte (Deemed to be University), Mangalore, Karnataka, India
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Ali A, Saqib F. Ethnopharmacological basis and pharmacodynamics prospectives for folkloric claims of Rosa webbiana wall. Ex. Royle in diarrhea and asthma via In vitro, In vivo and In silico techniques. JOURNAL OF ETHNOPHARMACOLOGY 2023; 317:116696. [PMID: 37315649 DOI: 10.1016/j.jep.2023.116696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 05/19/2023] [Accepted: 05/28/2023] [Indexed: 06/16/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Rosa webbiana (Family: Rosaceae) is used by South Asian herbalists to treat gastrointestinal and respiratory disorders. AIM OF THE STUDY This research aimed at multiple targets to verify R. webbiana for treating diarrhea and asthma. In vitro, in vivo, and in silico experiments were planned to demonstrate the antispasmodic and bronchodilator potential of R. webbiana. MATERIALS AND METHODS The bioactive compounds of R. webbiana were identified and quantified through LC ESI-MS/MS and HPLC. These compounds were predicted for muti-mechanisms of bronchodilator and antispasmodic potential in network pharmacology and molecular docking. In vitro methods (isolated rabbit trachea, bladder, and jejunum tissues) confirmed these multi-mechanisms for antispasmodic and bronchodilator effects. Antiperistalsis, antidiarrheal, and antisecretory experiments were conducted in in-vivo experiments. RESULTS The phytochemical analysis indicates the presence of rutin (742.91 μg/g), kaempferol (726.32 μg/g), and quercitrin (688.20 μg/g) in Rw. EtOH. These bioactive compounds in network pharmacology interfere with the pathogenic genes of diarrhea and asthma, which are the members of calcium-mediated signaling pathways and showed the stronger binding affinity towards voltage-gated L-type calcium channels, myosin light chain-kinase, Calcium calmodulin-dependent-kinase, Phosphodiesterase-4, and phosphoinositide phospholipase-C in molecular docking. Rw. EtOH elicited a spasmolytic response in isolated jejunum, trachea, and urine preparations by relaxing K+ (80 mM) and CCh (1 μM) spastic contractions. Additionally, it suppressed calcium concentration-response curves to the right, like verapamil. Like dicyclomine, it caused a rightward parallel shift of the CCh curves, followed by a non-parallel shift at higher concentrations with suppression of the maximal response. Like papaverine, it also caused isoprenaline-induced inhibitory CRCs to shift to the left. Verapamil did not potentiate isoprenaline-induced inhibitory CRCs, although it was more efficacious against K+ (80 mM) than CCh (1 μM)-induced contractions. R. webbiana EtOH extract exhibited complete antiperistalsis (21.55%), antidiarrheal (80.33%), and antisecretory (82.59±0.60) activities in vivo experiments at the dose of 300 mg/kg. CONCLUSION Thus, Rw. EtOH modulated multiple pathways, produced calcium antagonistic, anticholinergic, and phosphodiesterase inhibitory actions, and had antidiarrheal and bronchodilator effects.
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Affiliation(s)
- Anam Ali
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan (60000) Pakistan.
| | - Fatima Saqib
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan (60000) Pakistan.
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Iqbal I, Saqib F, Latif MF, Shahzad H, Dima L, Sajer B, Manea R, Pojala C, Necula R. Pharmacological Basis for Antispasmodic, Bronchodilator, and Antidiarrheal Potential of Dryopteris ramosa (Hope) C. via In Vitro, In Vivo, and In Silico Studies. ACS OMEGA 2023; 8:26982-27001. [PMID: 37546625 PMCID: PMC10398851 DOI: 10.1021/acsomega.3c01907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/21/2023] [Indexed: 08/08/2023]
Abstract
Background:Dryopteris ramosa is used as an old treatment for several diseases. D. ramose fronds are eaten to treat gastrointestinal (GIT) issues and as an antibiotic. However, there is a dearth of literature justifying its traditional use. Aims and objectives: the current work used biological and molecular docking studies to support traditional usage and elucidate D. ramosa's multitarget mechanism. Materials and methods: Bioactive compounds were docked in silico. Force displacement transducers coupled with a power lab data gathering system examined the effects of compounds on rabbit jejunum, trachea, and aorta tissues. Albino mice and rats were used for in vivo studies. Results: Bioactive compounds interacted with inflammation, asthma, and diarrhea genes, according to in silico studies. D. ramosa crude extract (Dr.Cr) calmed impulsive contractions and K+ (80 mM)-provoked contractions in the jejunum and tracheal tissue dose-dependently, showing the presence of the Ca++ channel-blocking (CCB) effect, further verified by the rightward parallel shift of CRCs equivalent to verapamil. Polarity-based fractionation showed spasmolytic activity in Dr.DCM and muscarinic receptors mediated spasmogenic activity in the Dr.Aq fraction. Dr.Cr vasoconstricted the aortic preparation, which was totally blocked by an angiotensin II receptor antagonist. This suggests that Dr. Cr's contractile effect is mediated through angiotensin receptors. In rats and mice, it showed anti-inflammatory and antidiarrheal action. Conclusion: This study supports the traditional medicinal uses of D. ramosa against GIT disorders and may be an important therapeutic agent in the future.
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Affiliation(s)
- Iram Iqbal
- Department
of Pharmacology; Bahauddin Zakariya University, Multan 60000, Pakistan
| | - Fatima Saqib
- Department
of Pharmacology; Bahauddin Zakariya University, Multan 60000, Pakistan
| | | | - Hamna Shahzad
- Department
of Biochemistry, Bahauddin Zakariya University, Multan 60000, Pakistan
| | - Lorena Dima
- Faculty
of Medicine, Transilvania University of
Brasov, Brasov 500036, Romania
| | - Bayan Sajer
- Department
of Biological Sciences, College of Science, King Abdulaziz University, Jeddah 80200, Saudi Arabia
| | - Rosana Manea
- Faculty
of Medicine, Transilvania University of
Brasov, Brasov 500036, Romania
| | - Ciprian Pojala
- Faculty
of Medicine, Transilvania University of
Brasov, Brasov 500036, Romania
| | - Radu Necula
- Faculty
of Medicine, Transilvania University of
Brasov, Brasov 500036, Romania
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Khurm M, Guo Y, Wu Q, Zhang X, Ghori MU, Rasool MF, Imran I, Saqib F, Wahid M, Guo Z. Conocarpus lancifolius (Combretaceae): Pharmacological Effects, LC-ESI-MS/MS Profiling and In Silico Attributes. Metabolites 2023; 13:794. [PMID: 37512501 PMCID: PMC10385132 DOI: 10.3390/metabo13070794] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/17/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
In folklore medicine, Conocarpus lancifolius is used to treat various illnesses. The main objective of this study was a comprehensive investigation of Conocarpus lancifolius leaf aqueous extract (CLAE) for its antioxidant, cardioprotective, anxiolytic, antidepressant and memory-enhancing capabilities by using different in vitro, in vivo and in silico models. The in vitro experimentation revealed that CLAE consumed an ample amount of total phenolics (67.70 ± 0.15 µg GAE/mg) and flavonoids (47.54 ± 0.45 µg QE/mg) with stronger antiradical effects through DPPH (IC50 = 16.66 ± 0.42 µg/mL), TAC (77.33 ± 0.41 µg AAE/mg) and TRP (79.11 ± 0.67 µg GAE/mg) assays. The extract also displayed suitable acetylcholinesterase (AChE) inhibitory (IC50 = 110.13 ± 1.71 µg/mL) activity through a modified Ellman's method. The toxicology examination presented no mortality or any signs of clinical toxicity in both single-dose and repeated-dose tests. In line with the cardioprotective study, the pretreatment of CLAE was found to be effective in relieving the isoproterenol (ISO)-induced myocardial injury in rats by normalizing the heart weight index, serum cardiac biomarkers, lipid profile and various histopathological variations. In the noise-stress-induced model for behavior attributes, the results demonstrated that CLAE has the tendency to increase the time spent in the central zone and elevated open arms in the open field and elevated plus maze tests (examined for anxiety assessment), reduced periods of immobility in the forced swimming test (for depression) and improved recognition and working memory in the novel object recognition and Morris water maze tests, respectively. Moreover, the LC-ESI-MS/MS profiling predicted 53 phytocompounds in CLAE. The drug-likeness and ADMET analysis exhibited that the majority of the identified compounds have reasonable physicochemical and pharmacokinetic profiles. The co-expression of molecular docking and network analysis indicated that top-ranked CLAE phytoconstituents act efficiently against the key proteins and target multiple signaling pathways to exert its cardiovascular-protectant, anxiolytic, antidepressant and memory-enhancing activity. Hence, this artifact illustrates that the observed biological properties of CLAE elucidate its significance as a sustainable source of bioactive phytochemicals, which appears to be advantageous for pursuing further studies for the development of new therapeutic agents of desired interest.
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Affiliation(s)
- Muhammad Khurm
- School of Pharmacy, Xi'an Jiaotong University, Xi'an 710061, China
| | - Yuting Guo
- School of Pharmacy, Xi'an Jiaotong University, Xi'an 710061, China
| | - Qingqing Wu
- School of Pharmacy, Xi'an Jiaotong University, Xi'an 710061, China
| | - Xinxin Zhang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an 710061, China
| | - Muhammad Umer Ghori
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan
| | - Muhammad Fawad Rasool
- Department of Pharmacy Practice, Faculty of Pharmacy, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Imran Imran
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Fatima Saqib
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Muqeet Wahid
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Zengjun Guo
- School of Pharmacy, Xi'an Jiaotong University, Xi'an 710061, China
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Wadhwa K, Kaur H, Kapoor N, Brogi S. Identification of Sesamin from Sesamum indicum as a Potent Antifungal Agent Using an Integrated in Silico and Biological Screening Platform. Molecules 2023; 28:4658. [PMID: 37375219 DOI: 10.3390/molecules28124658] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Due to the limited availability of antifungal drugs, their relevant side effects and considering the insurgence of drug-resistant strains, novel antifungal agents are urgently needed. To identify such agents, we have developed an integrated computational and biological screening platform. We have considered a promising drug target in antifungal drug discovery (exo-1,3-β-glucanase) and a phytochemical library composed of bioactive natural products was used. These products were computationally screened against the selected target using molecular docking and molecular dynamics techniques along with the evaluation of drug-like profile. We selected sesamin as the most promising phytochemical endowed with a potential antifungal profile and satisfactory drug-like properties. Sesamin was submitted to a preliminary biological evaluation to test its capability to inhibit the growth of several Candida species by calculating the MIC/MFC and conducting synergistic experiments with the marketed drug fluconazole. Following the screening protocol, we identified sesamin as a potential exo-1,3-β-glucanase inhibitor, with relevant potency in inhibiting the growth of Candida species in a dose-dependent manner (MIC and MFC of 16 and 32 µg/mL, respectively). Furthermore, the combination of sesamin with fluconazole highlighted relevant synergistic effects. The described screening protocol revealed the natural product sesamin as a potential novel antifungal agent, showing an interesting predicted pharmacological profile, paving the way to the development of innovative therapeutics against fungal infections. Notably, our screening protocol can be helpful in antifungal drug discovery.
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Affiliation(s)
- Khushbu Wadhwa
- Fungal Biology Laboratory, Ramjas College, University of Delhi, Delhi 110007, India
| | - Hardeep Kaur
- Fungal Biology Laboratory, Ramjas College, University of Delhi, Delhi 110007, India
| | - Neha Kapoor
- Department of Chemistry, Hindu College, University of Delhi, Delhi 110007, India
| | - Simone Brogi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
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Hussain Shah SA, Aleem A. Investigations of plausible pharmacodynamics supporting the antispasmodic, bronchodilator, and antidiarrheal activities of Berberis lycium Royle. Via in silico, in vitro, and in vivo studies. JOURNAL OF ETHNOPHARMACOLOGY 2023; 305:116115. [PMID: 36587881 DOI: 10.1016/j.jep.2022.116115] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/23/2022] [Accepted: 12/24/2022] [Indexed: 06/17/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Berberis lycium Royle, a member of the Berberidaceae family, is a high-value medicinal plant with a documented history of usage in traditional medicine and has demonstrated significant therapeutic results among local populations throughout the globe. It is used traditionally in many parts of Pakistan to treat diarrhea, abdominal spasms, coughs, and chest problems. AIM OF THE STUDY To investigate the antispasmodic, bronchodilator, and antidiarrheal effects of B. lycium and its possible underlying mechanisms through in silico, in vitro, and in vivo studies. MATERIALS AND METHODS LC ESI-MS/MS analysis was used to identify bioactive components within the hydromethanolic extract of B. lycium. In silico studies, including network pharmacology and molecular docking, were utilized to investigate the antispasmodic and bronchodilator properties of the extract's bioactive components. In vitro pharmacological studies were conducted using isolated rabbit jejunum, trachea, urinary bladder, and rat ileum preparations. In vivo antidiarrheal activities were conducted in mice, including castor oil-induced diarrhea, intestinal transit, and castor oil-induced enteropooling. RESULTS The LC ESI-MS/MS analysis of the hydromethanolic extract of B. lycium identified 38 bioactive compounds. Network pharmacology study demonstrated that the mechanism of BLR for the treatment of diarrhea might involve IL1B, TLR4, PIK3R1, TNF, PTPRC, IL2, PIK3CD, and ABCB1, whereas, for respiratory ailments, it may involve PIK3CG, TRPV1, STAT3, ICAM1, ACE, PTGER2, PTGS2, TNF, MMP9, NOS2, IL2, CCR5, HRH1, and VDR. Molecular docking research revealed that chlorogenic acid, epigallocatechin, isorhamnetin, quinic acid, gallic acid, camptothecin, formononetin-7-O-glucoside, velutin, caffeic acid, and (S)-luteanine exhibited a higher docking score than dicyclomine with validated proteins of smooth muscle contractions such as CACB2_HUMAN, ACM3_HUMAN, MYLK_HUMAN, and PLCG1_HUMAN. In vitro investigations demonstrated that Blr.Cr, Blr.EtOAc, and Blr.Aq relaxed spontaneously contracting jejunum preparations; carbachol (1 μM)-induced and K+ (80 mM)-induced jejunum, trachea, and urinary bladder contractions in a concentration-dependent manner, similar to dicyclomine. Moreover, Blr.Cr, Blr.EtOAc, and Blr.Aq exhibited a rightward shift in Ca+2 and carbachol cumulative response curves, similar to dicyclomine, demonstrating the coexistence of antimuscarinic and Ca+2 antagonistic mechanisms due to the presence of alkaloids and flavonoids. In vivo antidiarrheal activities showed that the hydromethanolic extract was significantly effective against castor oil-induced diarrhea and castor oil-induced enteropooling, similar to loperamide, and charcoal meal intestinal transit, similar to atropine, in mice at doses of 50, 100, and 200 mg/kg body weight, which supports its traditional use in diarrhea. CONCLUSION The dual blocking mechanism of muscarinic receptors and Ca+2 channels behind the smooth muscle relaxing activity reveals the therapeutic relevance of B. lycium in diarrhea, abdominal spasms, coughs, and chest problems.
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Affiliation(s)
- Syed Adil Hussain Shah
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan, 60800, Pakistan.
| | - Ambreen Aleem
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan, 60800, Pakistan.
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Wahid M, Saqib F, Akhtar S, Ali A, Tallei TE, Simal-Gandara J. Mechanistic insights of Cucumis melo L. seeds for gastrointestinal muscle spasms through calcium signaling pathway-related gene regulation networks in WGCNA and in vitro, in vivo studies. Comput Biol Med 2023; 155:106596. [PMID: 36773554 DOI: 10.1016/j.compbiomed.2023.106596] [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: 11/28/2022] [Revised: 12/26/2022] [Accepted: 01/22/2023] [Indexed: 02/05/2023]
Abstract
BACKGROUND In addition to the nutritional benefits of Cucumis melo L., herbalists in Pakistan and India employ seeds to treat various ailments. This study aimed to determine the regulatory role of C. melo seeds in calcium-mediated smooth muscle contraction. METHODS We identified and quantified the phytochemicals of C. melo with LC ESI-MS/MS and HPLC, then conducted in vitro and in vivo tests to confirm the involvement in smooth muscle relaxation. Then, diarrhea-predominant irritable bowel syndrome gene datasets from NCBI GEO were acquired, DEGs and WGCNA followed by functional enrichment analysis. Next, molecular docking of key genes was performed. RESULTS The quantification of C. melo seeds revealed concentrations of rutin, kaempferol, and quercetin were 702.38 μg/g, 686.29 μg/g, and 658.41 μg/g, respectively. In vitro experiments revealed that C. melo seeds had a dose-dependent relaxant effect for potassium chloride (80 mM)-induced spastic contraction and exhibited calcium antagonistic response in calcium dose-response curves. In in vivo studies, Cm.EtOH exhibited antidiarrheal, antiperistaltic, and antisecretory effects. The functional enrichment of WGCNA and DEGs IBS-associated pathogenic genes, including those involved in calcium-mediated signaling, MAPK cascade, and inflammatory responses. MAPK1 and PIK3CG were identified as key genes with greater binding affinity with rutin, quercitrin, and kaempferol in molecular docking. CONCLUSIONS The bronchodilator and antidiarrheal effects of C. melo were produced by altering the regulatory genes of calcium-mediated smooth contraction.
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Affiliation(s)
- Muqeet Wahid
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan, 60000, Pakistan.
| | - Fatima Saqib
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan, 60000, Pakistan.
| | - Saeed Akhtar
- Institute of Food Science and Nutrition, Bahauddin Zakariya University, Multan, 60000, Pakistan.
| | - Anam Ali
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan, 60000, Pakistan.
| | - Trina Ekawati Tallei
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado, 95115, North Sulawesi, Indonesia.
| | - Jesus Simal-Gandara
- Universidade de Vigo, Nutrition and Bromatology Group, Analytical Chemistry and Food Science Department, Faculty of Science, E32004, Ourense, Spain.
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Sharma S, Kumar P. Decoding the Role of MDM2 as a Potential Ubiquitin E3 Ligase and Identifying the Therapeutic Efficiency of Alkaloids against MDM2 in Combating Glioblastoma. ACS OMEGA 2023; 8:5072-5087. [PMID: 36777618 PMCID: PMC9910072 DOI: 10.1021/acsomega.2c07904] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/17/2023] [Indexed: 05/28/2023]
Abstract
Glioblastomas (GBMs) represent the most aggressive form of brain tumor arising from the malignant transformation of astrocytes. Despite various advancements, treatment options remain limited to chemotherapy and radiotherapy followed by surgery giving an overall survival of 14-15 months. These therapies are somewhere restricted in giving a better survival and cure. There is a need for new therapeutics that could potentially target GBM based on molecular pathways and pathology. Here, ubiquitin E3 ligases can be used as targets as they bind a wide array of substrates and therefore can be attractive targets for new inhibitors. Through this study, we have tried to sort various ubiquitin E3 ligases based on their expression, pathways to which these ligases are associated, and mutational frequencies, and then we tried to screen potent inhibitors against the most favorable E3 ligase as very few studies are available concerning inhibition of E3 ligase in GBM. Our study found MDM2 to be the most ideal E3 ligase and further we tried to target MDM2 against various compounds under the alkaloid class. Molecular Docking and MD simulations combined with ADMET properties and BBB scores revealed that only evodiamine and sanguinarine were effective in inhibiting MDM2. We also tried to give a proposed mechanism of how these inhibitors mediate the p53 signaling in GBM. Therefore, the new scaffolds predicted by the computational approach could help in designing promising therapeutic agents targeting MDM2 in glioblastoma.
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Wahid M, Saqib F, Ali A, Alshammari A, Alharbi M, Rauf A, Mubarak MS. Integrated Mechanisms of Polarity-Based Extracts of Cucumis melo L. Seed Kernels for Airway Smooth Muscle Relaxation via Key Signaling Pathways Based on WGCNA, In Vivo, and In Vitro Analyses. Pharmaceuticals (Basel) 2022; 15:ph15121522. [PMID: 36558973 PMCID: PMC9784679 DOI: 10.3390/ph15121522] [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: 10/13/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022] Open
Abstract
The present study aimed to determine the mechanisms responsible for calcium-mediated smooth muscle contractions in C. melo seeds. The phytochemicals of C. melo were identified and quantified with the aid of Liquid Chromatography Electrospray Ionization Tandem Mass Spectrometric (LC/ESI-MS/MS) and high-performance liquid chromatography (HPLC), and then tested in-vitro and in vivo to confirm involvement in smooth muscle relaxation. Allergic asthma gene datasets were acquired from the NCBI gene expression omnibus (GEO) and differentially expressed gene (DEG) analysis, weighted gene co-expression network analysis (WGCNA), and functional enrichment analysis were conducted. Additionally, molecular docking of key genes was carried out. Kaempferol, rutin, and quercetin are identified as phytochemical constituents of C. melo seeds. Results indicated that C. melo seeds exhibit a dose-dependent relaxant effect for potassium chloride (80 mM)- induced spastic contraction and calcium antagonistic response in calcium dose-response curves. The functional enrichment of WGCNA and DEG asthma-associated pathogenic genes showed cytokine-mediated pathways and inflammatory responses. Furthermore, CACNA1A, IL2RB, and NOS2 were identified as key genes with greater binding affinity with rutin, quercitrin, and kaempferol in molecular docking. These results show that the bronchodilator and antidiarrheal effects of C. melo were produced by altering the regulatory genes of calcium-mediated smooth muscle contraction.
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Affiliation(s)
- Muqeet Wahid
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan 60000, Pakistan
| | - Fatima Saqib
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan 60000, Pakistan
- Correspondence: (F.S.); (M.S.M.)
| | - Anam Ali
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan 60000, Pakistan
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh 11451, Saudi Arabia
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdur Rauf
- Department of Chemistry, University of Swabi, Swabi 94640, Pakistan
| | - Mohammad S. Mubarak
- Department of Chemistry, The University of Jordan, Amma 11942, Jordan
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
- Correspondence: (F.S.); (M.S.M.)
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Ciccone L, Piragine E, Brogi S, Camodeca C, Fucci R, Calderone V, Nencetti S, Martelli A, Orlandini E. Resveratrol-like Compounds as SIRT1 Activators. Int J Mol Sci 2022; 23:ijms232315105. [PMID: 36499460 PMCID: PMC9738298 DOI: 10.3390/ijms232315105] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
The sirtuin 1 (SIRT1) activator resveratrol has emerged as a promising candidate for the prevention of vascular oxidative stress, which is a trigger for endothelial dysfunction. However, its clinical use is limited by low oral bioavailability. In this work, we have applied a previously developed computational protocol to identify the most promising derivatives from our in-house chemical library of resveratrol derivatives. The most promising compounds in terms of SIRT1 activation and oral bioavailability, predicted in silico, were evaluated for their ability to activate the isolated SIRT1 enzyme. Then, we assessed the antioxidant effects of the most effective derivative, compound 3d, in human umbilical vein endothelial cells (HUVECs) injured with H2O2 100 µM. The SIRT1 activator 3d significantly preserved cell viability and prevented an intracellular reactive oxygen species increase in HUVECs exposed to the oxidative stimulus. Such effects were partially reduced in the presence of a sirtuin inhibitor, sirtinol, confirming the potential role of sirtuins in the activity of resveratrol and its derivatives. Although 3d appeared less effective than resveratrol in activating the isolated enzyme, the effects exhibited by both compounds in HUVECs were almost superimposable, suggesting a higher ability of 3d to cross cell membranes and activate the intracellular target SIRT1.
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Affiliation(s)
- Lidia Ciccone
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
- Center for Instrument Sharing, University of Pisa (CISUP), Lungarno Pacinotti 43, 56126 Pisa, Italy
| | - Eugenia Piragine
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Simone Brogi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Caterina Camodeca
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Raffaele Fucci
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Vincenzo Calderone
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
- Center for Instrument Sharing, University of Pisa (CISUP), Lungarno Pacinotti 43, 56126 Pisa, Italy
| | - Susanna Nencetti
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
- Center for Instrument Sharing, University of Pisa (CISUP), Lungarno Pacinotti 43, 56126 Pisa, Italy
- Correspondence: (S.N.); (A.M.)
| | - Alma Martelli
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
- Center for Instrument Sharing, University of Pisa (CISUP), Lungarno Pacinotti 43, 56126 Pisa, Italy
- Correspondence: (S.N.); (A.M.)
| | - Elisabetta Orlandini
- Department of Earth Science, University of Pisa, Via Santa Maria 53, 56126 Pisa, Italy
- Research Centre E. Piaggio, University of Pisa, 56126 Pisa, Italy
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Wahid M, Saqib F, Qamar M, Ziora ZM. Antispasmodic activity of the ethanol extract of Citrullus lanatus seeds: Justifying ethnomedicinal use in Pakistan to treat asthma and diarrhea. JOURNAL OF ETHNOPHARMACOLOGY 2022; 295:115314. [PMID: 35490899 DOI: 10.1016/j.jep.2022.115314] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 03/25/2022] [Accepted: 04/18/2022] [Indexed: 06/14/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Citrullus lanatus (Thunb.) belongs to the ground family, Cucurbitaceae, known for edible fruit. Besides nutritional benefits, the traditional herbal practitioners in Pakistan and India used their seeds to treat gastrointestinal, respiratory, and urinary disorders. In Northern Sudan, its seeds are often used as a laxative. Its root is laxative and emetic at a high dose. Its seeds are also used to treat bedwetting and urinary tract obstruction. AIM OF THE STUDY This study aimed to elucidate the multi-target mechanisms of Citrullus lanatus seeds to treat asthma and diarrhea. The pharmacological experiments were designed and conducted, along with the pharmacology network and molecular docking predictions, to verify the seeds biopotency for antispasmodic and bronchodilator properties. METHODS LC ESI-MS/MS were performed to identify the potentially active compounds in hydroethanolic extract of Citrullus lanatus seeds, then to quantify them by HPLC. The quantified bioactive compounds of Citrullus lanatus, i.e., stigmasterol, quinic acid, malic acid, epicatechin, caffeic acid, rutin, p-coumaric acid, quercetin, ferulic acid, scopoletin, apigenin, and kaempferol were subjected to in silico studies for molecular docking. The hydroethanolic extract of Citrullus lanatus seeds was examined on isolated rabbit tissue, i.e., jejunum, trachea, and urinary bladder. The antiperistalsis, antidiarrheal and antisecretory studies were also performed in animal models. RESULTS In silico studies revealed that bioactive compounds of C. lanatus seeds interfere with asthma and diarrhea-associated target genes, which are a member of calcium mediate signaling, regulation of cytosolic calcium concentration, smooth muscle contraction, and inflammatory responses. It was also found that rutin, quercetin, kaempferol, and scopoletin were stronger binding to voltage-gated calcium channels, calcium/calmodulin-dependent protein kinase, myosin light chain kinase, and phosphoinositide phospholipase C, thus, exerting calcium channel blocker activity. The hydroethanolic extract of C. lanatus seeds exerted a concentration-dependent relaxant response for the spasmolytic response on isolated jejunum and trachea preparations and caused relaxation of spastic contraction of K+ (80 mM). Furthermore, it caused a non-parallel rightward shift with suppression of calcium concentration-response curves. In animal models, the Cl.EtOH showed antiperistalsis, antidiarrheal and antisecretory response. CONCLUSION Thus, we confirm Citrullus lanatus seeds have some medicinal effects by regulating the contractile response through target proteins of calcium mediates signaling and can be a promising component in the medical treatment for asthma and diarrhea.
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Affiliation(s)
- Muqeet Wahid
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan, 60000, Pakistan
| | - Fatima Saqib
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan, 60000, Pakistan.
| | - Muhammad Qamar
- Institute of Food Science and Nutrition, Bahauddin Zakariya University, Multan, 60000, Pakistan
| | - Zyta M Ziora
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
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Saqib F, Wahid M, Al-Huqail AA, Ahmedah HT, Bigiu N, Irimie M, Moga M, Marc Vlaic RA, Pop OL, Chicea LM. Metabolomics based mechanistic insights to vasorelaxant and cardioprotective effect of ethanolic extract of Citrullus lanatus (Thunb.) Matsum. & Nakai. seeds in isoproterenol induced myocardial infraction. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 100:154069. [PMID: 35364560 DOI: 10.1016/j.phymed.2022.154069] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 02/14/2022] [Accepted: 03/19/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Cardiovascular diseases (CVDs) are a significant cause of morbidity and death in the current world, posing a challenge to both developing and industrialized nation's health systems. Citrullus lanatus (Thunb.) Matsum. & Nakai. seeds have long been utilized to supplement and enhance health and treat cardiovascular illnesses. However, its treatments for CVDs are still unknown. More research is required to fully comprehend the impact of C. lanatus seeds on vasorelaxation and myocardial infractions. PURPOSE Therefore, an integrated metabolomics profiling technique was used to investigate possible pathways of C. lanatus in isoproterenol (ISO)-induced myocardial infarction (MI). Isoproterenol causes long-term cardiac hypertrophy by causing cardiomyocyte compensatory loss, eventually leading to heart failure. METHODS In vitro models of vasoconstriction, atrium, and in vivo models of invasive blood pressure measurement and isoproterenol (ISO) induced cardiac hypertrophy in rats were used to understand underlying mechanistic by LC-MS/MS based dynamic metabolomics analysis of the serum and heart samples to be investigated the effect of ethanolic extract of C. lanatus (Cl.EtOH). RESULTS Cl.EtOH exhibited vasorelaxant, negative chronotropic, and inotropic effects in in-vitro models whereas, a potent hypotensive effect was observed in normotensive rats. The Cl.EtOH protected the animals from ISO-induced myocardial infarction (MI) with therapeutic interventions in left ventricular thickness, cardiomyocyte hypertrophy, mRNA gene expression, biochemical assays, and metabolomic profiling of serum and heart tissues. CONCLUSIONS For the first time, our study confirmed that C. lanatus seeds (Cl.EtOH) possess significant antihypertensive and prevent ISO-induced myocardial infarction. These findings comprehensively demonstrated mechanistic insights of Cl.EtOH in vasorelaxation and myocardial infarction. The current study provides evidence for further mechanistic studies and the development of C. lanatus seeds as a potential therapeutic intervention for patients with cardiovascular disorders.
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Affiliation(s)
- Fatima Saqib
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan, Pakistan
| | - Muqeet Wahid
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan, Pakistan
| | - Arwa Abdulkreem Al-Huqail
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia.
| | - Hanadi Talal Ahmedah
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Rabigh 25732, Saudi Arabia
| | - Nicusor Bigiu
- Faculty of Medicine, Transilvania University of Brasov, 500019 Brasov.
| | - Marius Irimie
- Faculty of Medicine, Transilvania University of Brasov, 500019 Brasov
| | - Marius Moga
- Faculty of Medicine, Transilvania University of Brasov, 500019 Brasov
| | - Romina Alina Marc Vlaic
- Food Engineering Department, Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine, 400372 Cluj-Napoca, Romania.
| | - Oana Lelia Pop
- Department of Food Science, University of Agricultural Science and Veterinary Medicine, 400372 Cluj-Napoca, Romania
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Possible Mechanisms Underlying the Antispasmodic, Bronchodilator, and Antidiarrheal Activities of Polarity-Based Extracts of Cucumis sativus L. Seeds in In Silico, In Vitro, and In Vivo Studies. Pharmaceuticals (Basel) 2022; 15:ph15050641. [PMID: 35631468 PMCID: PMC9143705 DOI: 10.3390/ph15050641] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 04/29/2022] [Accepted: 05/09/2022] [Indexed: 02/06/2023] Open
Abstract
Apart from the nutritional value, Cucumis sativus L. has also been used in the traditional medicine of Iran, Pakistan, and India. Its seeds are used by herbalists to treat gastrointestinal, respiratory, and urinary problems. However, more investigations are required to explain its mechanisms for treating GI, respiratory, and urinary diseases. Accordingly, the aim of the present work was to investigate the antispasmodic, bronchodilator, and antidiarrheal activities of C. sativus seeds extracts and the underlying mechanisms of action. For this purpose, sequential extracts of C. sativus seeds were prepared in n-hexane, dichloromethane, ethanol, and water. Bioactive compounds in C. sativus seed extracts were identified and quantified by utilizing LC ESI–MS/MS and HPLC. Moreover, network pharmacology and molecular docking were employed to examine the antispasmodic and bronchodilator effects of the bioactive substances in the extracts. In vitro and in vivo experiments were also conducted to validate the mechanistic insights gained from the in silico analysis. Results indicated the presence of kaempferol with a concentration of 813.74 µg/g (highest concentration) in the seed extract of C. sativus, followed by quercetin (713.83 µg/g), narcissin (681.87 µg/g), and orientin (676.19 µg/g). In silico investigations demonstrated that the bioactive chemicals in C. sativus seeds inhibited the expression of the target genes involved in smooth muscle contraction and calcium-mediated signaling. Sequential seed extracts of C. sativus caused a dose-dependent relaxant response for spasmolytic reaction and resulted in a relaxation of K+ (80 mM) spastic contraction. In animal models, C. sativus seed extracts exhibited partial or complete antiperistalsis, antidiarrheal, and antisecretory actions. By modulating the contractile response through calcium-mediated signaling target proteins, C. sativus seeds generated bronchodilator, antispasmodic, and antidiarrheal therapeutic effects.
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Oyedele AQK, Adelusi TI, Ogunlana AT, Adeyemi RO, Atanda OE, Babalola MO, Ashiru MA, Ayoola IJ, Boyenle ID. Integrated virtual screening and molecular dynamics simulation revealed promising drug candidates of p53-MDM2 interaction. J Mol Model 2022; 28:142. [PMID: 35536362 DOI: 10.1007/s00894-022-05131-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 04/28/2022] [Indexed: 12/13/2022]
Abstract
In the vast majority of malignancies, the p53 tumor suppressor pathway is compromised. In some cancer cells, high levels of MDM2 polyubiquitinate p53 and mark it for destruction, thereby leading to a corresponding downregulation of the protein. MDM2 interacts with p53 via its hydrophobic pocket, and chemical entities that block the dimerization of the protein-protein complex can restore p53 activity. Thus far, only a few chemical compounds have been reported as potent arsenals against p53-MDM2. The Protein Data Bank has crystallogaphic structures of MDM2 in complex with certain compounds. Herein, we have exploited one of the complexes in the identification of new p53-MDM2 antagonists using a hierarchical virtual screening technique. The initial stage was to compile a targeted library of structurally appropriate compounds related to a known effective inhibitor, Nutlin 2, from the PubChem database. The identified 57 compounds were subjected to virtual screening using molecular docking to discover inhibitors with high binding affinity for MDM2. Consequently, five compounds with higher binding affinity than the standard emerged as the most promising therapeutic candidates. When compared to Nutlin 2, four of the drug candidates (CID_140017825, CID_69844501, CID_22721108, and CID_22720965) demonstrated satisfactory pharmacokinetic and pharmacodynamic profiles. Finally, MD simulation of the dynamic behavior of lead-protein complexes reveals the stability of the complexes after a 100,000 ps simulation period. In particular, when compared to the other three leads, overall computational modeling found CID_140017825 to be the best pharmacological candidate. Following thorough experimental trials, it may emerge as a promising chemical entity for cancer therapy.
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Affiliation(s)
- Abdul-Quddus Kehinde Oyedele
- Computational Biology/Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomosho, Nigeria.,Department of Biochemistry and Nutrition, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
| | - Temitope Isaac Adelusi
- Computational Biology/Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomosho, Nigeria
| | - Abdeen Tunde Ogunlana
- Computational Biology/Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomosho, Nigeria
| | - Rofiat Oluwabusola Adeyemi
- Computational Biology/Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomosho, Nigeria.,Department of Biochemistry and Nutrition, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
| | - Opeyemi Emmanuel Atanda
- Computational Biology/Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomosho, Nigeria
| | | | - Mojeed Ayoola Ashiru
- Department of Chemical Sciences, Biochemistry Unit, College of Natural and Applied Science, Fountain University, Osogbo, Nigeria
| | - Isong Josiah Ayoola
- Department of Biochemistry and Nutrition, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
| | - Ibrahim Damilare Boyenle
- Computational Biology/Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomosho, Nigeria. .,College of Health Sciences, Crescent University, Abeokuta, Nigeria.
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Wahid M, Saqib F. Scientific basis for medicinal use of Citrullus lanatus (Thunb.) in diarrhea and asthma: In vitro, in vivo and in silico studies. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 98:153978. [PMID: 35158236 DOI: 10.1016/j.phymed.2022.153978] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 01/10/2022] [Accepted: 02/02/2022] [Indexed: 05/27/2023]
Abstract
BACKGROUND Citrullus lanatus (Thunb.) is a member of the Cucurbitaceae family, commonly farmed as an edible vegetable around the globe. It has been used in traditional therapies in addition to nutritional advantages. Traditional herbal practitioners employ C. lanatus seeds to treat gastrointestinal, respiratory, and urinary diseases in Pakistan and India. However, more investigation is needed to understand the effect of C. lanatus seeds on treating gastrointestinal, respiratory, and urinary disorders. PURPOSE This research aimed to use network pharmacology and molecular docking to understand multi-target mechanisms of C. lanatus seeds against asthma and diarrhea and to validate its effects using biological tests to investigate antispasmodic and bronchodilator capabilities. METHODS The ground seeds of C. lanatus were extracted in hexane, dichloromethane, ethanol, and aqueous for sequential extracts. The bioactive components in sequential extracts of C. lanatus seeds were identified using LC ESI-MS/MS, and specific compounds were quantified using HPLC. The quantified bioactive compounds of C. lanatus were subjected to in silico studies for network pharmacology and molecular docking to elucidate their role in antispasmodic and bronchodilator properties. The sequential extracts were tested on isolated rabbit tissue, i.e., jejunum, trachea, and urinary bladder. The antiperistalsis, antidiarrheal and antisecretory studies were also performed in animal models. RESULTS In silico studies indicate that bioactive chemicals from sequential extracts of C. lanatus seeds interfere with asthma and diarrhea-associated pathogenic genes. Those are members of calcium mediate signaling, cholinergic synapse, regulation of cytosolic calcium concentration, smooth muscle contraction, and inflammatory responses. It was also found that rutin, quercitrin, stearic acid, umbelliferone, and kaempferol were stronger binding to voltage-gated calcium channels and muscarinic M3 receptor, thus exerting calcium channel blocker activity and cholinergic receptor stimulant response. On isolated jejunum, trachea, and urinary preparations, sequential extracts of C. lanatus seeds elicited the spasmolytic response and showed the relaxation of spastic contractions of K+ (80 mM) and carbachol (1 µM). Furthermore, it induced a non-parallel rightward shift in calcium concentration-response curves with suppression. In animal models, C. lanatus seed extracts exhibited partially or completely antiperistalsis, antidiarrheal, and antisecretory effects. CONCLUSION Thus, Citrullus lanatus had therapeutic benefits by modulating the contractile response through calcium-mediated signaling target proteins, hence exerting bronchodilator and antidiarrheal properties. The current study provides evidence for further mechanistic studies and the development of C. lanatus seeds as a potential therapeutic intervention for patients with gastrointestinal, respiratory, and urinary disorders.
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Affiliation(s)
- Muqeet Wahid
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan (60000), Pakistan
| | - Fatima Saqib
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan (60000), Pakistan.
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18
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Wahid M, Saqib F, Chicea L, Ahmedah HT, Sajer BH, Marc Vlaic RA, Pop OL, Moga M, Gavris C. Metabolomics analysis delineates the therapeutic effects of hydroethanolic extract of Cucumis sativus L. seeds on hypertension and isoproterenol-induced myocardial infarction. Biomed Pharmacother 2022; 148:112704. [PMID: 35180666 DOI: 10.1016/j.biopha.2022.112704] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/31/2022] [Accepted: 02/04/2022] [Indexed: 02/08/2023] Open
Abstract
Cucumis sativus L., widely cultivated as an edible vegetable. Its seeds are well reputed for cardiovascular preventive properties. However, the mechanisms underlying for cardiovascular protection of C. sativus are still unidentified. Therefore, this study utilized a metabolomics approach to investigate putative mechanisms of C. sativus seeds in myocardial infarction (MI) and in vitro models of vasoconstriction, atrium, and invasive blood pressure measurement. Results showed that Cu.EtOH extract showed a vasorelaxant response with potent hypotensive effect in normotensive rats and L-NAME induced hypertension. Cu.EtOH caused a negative inotropic and positive chronotropic effect on the atrium. Cu.EtOH protected the animals from ISO-induced myocardial infarction (MI) interventions in left ventricular thickness, cardiomyocyte hypertrophy, mRNA gene expression, and biochemical assays. The metabolomics data suggested that Cu.EtOH mainly affected amino acid metabolism, BCAA degradation, ketone bodies degradation, and oxidative stress. Our study showed that Cu.EtOH suppressed inflammation with a strong anti-myocardial infarction impact. Additionally, our findings indicated Cu.EtOH reverted the amino acid metabolism, BCAA, and ketone bodies degradation. The findings show the antihypertensive mechanism of Cu.EtOH may include the modulation of endothelium-derived relaxing factor (EDRF) produced from nitric oxide (NO) and is connected with vascular endothelial function. C. sativus seeds, in particular, played a pivotal role in the treatment of myocardial and vascular disorders by enhancing the EDRF mechanism, energy generation, and antioxidant capacity. In summary, our findings showed the mechanistic insights on the therapeutic potential of C. sativus seeds for cardiovascular disorders.
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Affiliation(s)
- Muqeet Wahid
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan, Pakistan.
| | - Fatima Saqib
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan, Pakistan.
| | - Liana Chicea
- Faculty of Medicine, Lucian Blaga University of Sibiu, 2A Lucian Blaga Str., 550169 Sibiu, Romania.
| | - Hanadi Talal Ahmedah
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Rabigh 25732, Saudi Arabia.
| | - Bayan Hussein Sajer
- Department of Biological Sciences, King Abdulaziz University, Jeddah 80200, Saudi Arabia.
| | - Romina Alina Marc Vlaic
- Departament of Food Engineering, Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine, 400372 Cluj-Napoca, Romania.
| | - Oana Lelia Pop
- Department of Food Science, Faculty of Food Science and Technology, University of Agricultural Science and Veterinary Medicine, 400372 Cluj-Napoca, Romania.
| | - Marius Moga
- Faculty of Medicine, Transilvania University of Brasov, Romania.
| | - Claudia Gavris
- Faculty of Medicine, Transilvania University of Brasov, Romania.
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Saqib F, Usman F, Malik S, Bano N, Ur-Rahman N, Riaz M, Marc (Vlaic) RA, Mureşan CC. Antidiarrheal and Cardio-Depressant Effects of Himalaiella heteromalla (D.Don) Raab-Straube: In Vitro, In Vivo, and In Silico Studies. PLANTS 2021; 11:plants11010078. [PMID: 35009082 PMCID: PMC8747237 DOI: 10.3390/plants11010078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 11/16/2022]
Abstract
Himalaiella heteromalla (D.Don) Raab-Straube is a commonly used remedy against various diseases. Crude extract and fractions of H. heteromalla were investigated for a gastrointestinal, bronchodilator, cardiovascular, and anti-inflammatory activities. H. heteromalla crude extract (Hh.Cr) relaxed spontaneous contractions and K+ (80 mM)-induced contraction in jejunum tissue dose-dependently. The relaxation of K+ (80 mM) indicates the presence of Ca++ channel blocking (CCB) effect, which was further confirmed by constructing calcium response curves (CRCs) as they caused rightward parallel shift of CRCs in a manner comparable to verapamil, so the spasmolytic effect of Hh.Cr was due to its CCB activity. Application of Hh.Cr on CCh (1 µM) and K+ (80 mM)-induced contraction in tracheal preparation resulted in complete relaxation, showing its bronchodilator effect mediated through Ca++ channels and cholinergic antagonist activity. Application of Hh.Cr on aortic preparations exhibited vasorelaxant activity through angiotensin and α-adrenergic receptors blockage. It also showed the cardio suppressant effect with negative chronotropic and inotropic response in paired atrium preparation. Similar effects were observed in in vivo models, i.e., decreased propulsive movement, wet feces, and inhibition of edema formation.
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Affiliation(s)
- Fatima Saqib
- Faculty of Pharmacy, Bahauddin Zakariya University, Multan 60000, Pakistan; (F.U.); (S.M.)
- Correspondence: (F.S.); (R.A.M.)
| | - Faisal Usman
- Faculty of Pharmacy, Bahauddin Zakariya University, Multan 60000, Pakistan; (F.U.); (S.M.)
| | - Shehneela Malik
- Faculty of Pharmacy, Bahauddin Zakariya University, Multan 60000, Pakistan; (F.U.); (S.M.)
| | - Naheed Bano
- Faculty of Veterinary and Animal Sciences, MNS-University of Agriculture, Multan 60000, Pakistan;
| | - Najm Ur-Rahman
- Department of Pharmacy, Shaheed Benazir Bhutto University, Sheringal 18050, Pakistan; (N.U.-R.); (M.R.)
| | - Muhammad Riaz
- Department of Pharmacy, Shaheed Benazir Bhutto University, Sheringal 18050, Pakistan; (N.U.-R.); (M.R.)
| | - Romina Alina Marc (Vlaic)
- Food Engineering Department, Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine, 400372 Cluj-Napoca, Romania;
- Correspondence: (F.S.); (R.A.M.)
| | - Crina Carmen Mureşan
- Food Engineering Department, Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine, 400372 Cluj-Napoca, Romania;
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Hit Identification of a Novel Quinazoline Sulfonamide as a Promising EphB3 Inhibitor: Design, Virtual Combinatorial Library, Synthesis, Biological Evaluation, and Docking Simulation Studies. Pharmaceuticals (Basel) 2021; 14:ph14121247. [PMID: 34959648 PMCID: PMC8708751 DOI: 10.3390/ph14121247] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 11/17/2022] Open
Abstract
EphB3 is a major key player in a variety of cellular activities, including cell migration, proliferation, and apoptosis. However, the exact role of EphB3 in cancer remains ambiguous. Accordingly, new EphB3 inhibitors can increase the understanding of the exact roles of the receptor and may act as promising therapeutic candidates. Herein, a hybrid approach of structure-based design and virtual combinatorial library generated 34 quinazoline sulfonamides as potential selective EphB3 inhibitors. A molecular docking study over EphB3 predicted the binding affinities of the generated library, and the top seven hit compounds (3a and 4a–f), with GlideScore ≥ −6.20 Kcal/mol, were chosen for further MM-GBSA calculations. Out of the seven top hits, compound 4c showed the highest MM-GBSA binding free energy (−74.13 Kcal/mol). To validate these predicted results, compounds 3a and 4a–f were synthesized and characterized using NMR, HRMS, and HPLC. The biological evaluation revealed compound 4c as a potent EphB3 inhibitory lead (IC50 = 1.04 µM). The screening of 4c over a mini-panel of kinases consisting of EGFR, Aurora A, Aurora B, CDK2/cyclin A, EphB1, EphB2, EphB4, ERBB2/HER2, and KDR/VEGFR2, showed a promising selective profile against EphB3 isoform. A dose-dependent assay of compound 4c and a molecular docking study over the different forms of EphB provided insights into the elicited biological activities and highlighted reasonable explanations of the selectivity.
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21
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Wahid M, Saqib F, Ahmedah HT, Gavris CM, De Feo V, Hogea M, Moga M, Chicea R. Cucumis sativus L. Seeds Ameliorate Muscular Spasm-Induced Gastrointestinal and Respiratory Disorders by Simultaneously Inhibiting Calcium Mediated Signaling Pathway. Pharmaceuticals (Basel) 2021; 14:1197. [PMID: 34832981 PMCID: PMC8624829 DOI: 10.3390/ph14111197] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 11/18/2022] Open
Abstract
Cucumis sativus L. is globally cultivated as an edible vegetable. Besides its nutritional benefits, it is used in traditional medicines against various ailments. The current study was designed to elucidate the multi-target mechanisms of a C. sativus seeds extract against asthma and diarrhea using network pharmacology along with a molecular docking approach. Furthermore, in-vitro and in-vivo experiments were conducted to verify the mechanistic insight of in silico studies. LC-ESI-MS/MS was performed to identify the bioactive compounds in the extract; later, some compounds were quantified by HPLC. C. sativus seed. EtOH has kaempferol in higher concentration 783.02 µg/g, followed by quercetin (693.83 µg/g) and luteolin (617.17 µg/g). In silico studies showed that bioactive compounds interfered with asthma and diarrhea-associated target genes, which are members of calcium-mediated signaling to exert a calcium channel blocker activity. The seeds extract exerted a concentration-dependent spasmolytic response on isolated jejunum, trachea, and urinary bladder preparations and caused relaxation of spastic contraction of K+ (80 mM) with suppressed calcium concentration-response curves at dose 0.3 and 1 mg/mL. It also showed antiperistalsis, antidiarrheal and antisecretory activity in animal models. Thus, C. sativus seeds have therapeutic effects by regulating the contractile response through a calcium-mediated signaling pathway.
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Affiliation(s)
- Muqeet Wahid
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan 60800, Pakistan; (M.W.); (F.S.)
| | - Fatima Saqib
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan 60800, Pakistan; (M.W.); (F.S.)
| | - Hanadi Talal Ahmedah
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Rabigh 25732, Saudi Arabia;
| | - Claudia Mihaela Gavris
- Faculty of Medicine, Transilvania University of Brasov, 500036 Brasov, Romania; (M.H.); (M.M.)
| | - Vincenzo De Feo
- Department of Pharmacy, Salerno University, Fisciano, 84084 Salerno, Italy
| | - Mircea Hogea
- Faculty of Medicine, Transilvania University of Brasov, 500036 Brasov, Romania; (M.H.); (M.M.)
| | - Marius Moga
- Faculty of Medicine, Transilvania University of Brasov, 500036 Brasov, Romania; (M.H.); (M.M.)
| | - Radu Chicea
- Faculty of Medicine, Lucian Blaga University, 550024 Sibiu, Romania;
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22
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Sirous H, Campiani G, Calderone V, Brogi S. Discovery of novel hit compounds as potential HDAC1 inhibitors: The case of ligand- and structure-based virtual screening. Comput Biol Med 2021; 137:104808. [PMID: 34478925 DOI: 10.1016/j.compbiomed.2021.104808] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/24/2021] [Accepted: 08/24/2021] [Indexed: 11/28/2022]
Abstract
Histone deacetylases (HDACs) as an important family of epigenetic regulatory enzymes are implicated in the onset and progression of carcinomas. As a result, HDAC inhibition has been proven as a compelling strategy for reversing the aberrant epigenetic changes associated with cancer. However, non-selective profile of most developed HDAC inhibitors (HDACIs) leads to the occurrence of various side effects, limiting their clinical utility. This evidence provides a solid ground for ongoing research aimed at identifying isoform-selective inhibitors. Among the isoforms, HDAC1 have particularly gained increased attention as a preferred target for the design of selective HDACIs. Accordingly, in this paper, we have developed a reliable virtual screening process, combining different ligand- and structure-based methods, to identify novel benzamide-based analogs with potential HDAC1 inhibitory activity. For this purpose, a focused library of 736,160 compounds from PubChem database was first compiled based on 80% structural similarity with four known benzamide-based HDAC1 inhibitors, Mocetinostat, Entinostat, Tacedinaline, and Chidamide. Our inclusive in-house 3D-QSAR model, derived from pharmacophore-based alignment, was then employed as a 3D-query to discriminate hits with the highest predicted HDAC1 inhibitory activity. The selected hits were subjected to subsequent structure-based approaches (induced-fit docking (IFD), MM-GBSA calculations and molecular dynamics (MD) simulation) to retrieve potential compounds with the highest binding affinity for HDAC1 active site. Additionally, in silico ADMET properties and PAINS filtration were also considered for selecting an enriched set of the best drug-like molecules. Finally, six top-ranked hit molecules, CID_38265326, CID_56064109, CID_8136932, CID_55802151, CID_133901641 and CID_18150975 were identified to expose the best stability profiles and binding mode in the HDAC1 active site. The IFD and MD results cooperatively confirmed the interactions of the promising selected hits with critical residues within HDAC1 active site. In summary, the presented computational approach can provide a set of guidelines for the further development of improved benzamide-based derivatives targeting HDAC1 isoform.
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Affiliation(s)
- Hajar Sirous
- Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, 81746-73461 Isfahan, Iran.
| | - Giuseppe Campiani
- Department of Excellence of Biotechnology, Chemistry and Pharmacy, 2018-2022, University of Siena, Via Aldo Moro 2, I-53100 Siena, Italy
| | - Vincenzo Calderone
- Department of Pharmacy, University of Pisa, Via Bonanno 6, I-56126 Pisa, Italy
| | - Simone Brogi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, I-56126 Pisa, Italy.
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23
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Moreira J, Almeida J, Loureiro JB, Ramos H, Palmeira A, Pinto MM, Saraiva L, Cidade H. A Diarylpentanoid with Potential Activation of the p53 Pathway: Combination of in silico Screening Studies, Synthesis, and Biological Activity Evaluation. ChemMedChem 2021; 16:2969-2981. [PMID: 34170069 DOI: 10.1002/cmdc.202100337] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/21/2021] [Indexed: 11/07/2022]
Abstract
In silico studies of a library of diarylpentanoids led us to the identification of potential new MDM2/X ligands. The diarylpentanoids with the best docking scores obeying the druglikeness and ADMET prediction properties were subsequently synthesized and evaluated for their antiproliferative activity on colon cancer HCT116 and fibroblasts HFF-1 cells. The effect on p53-MDM2/X interactions was evaluated through yeast-based assays for compounds showing potent antiproliferative activity in HCT116 cells and low toxicity in normal cells, resulting in the identification of a potential dual inhibitor. Moreover, its antiproliferative effect was significantly reduced in the absence of p53 and in MDA-MB-231 cells expressing a mutant p53 form. The antiproliferative effect of this compound was associated with induction of cell cycle arrest, apoptosis, PARP cleavage and increased p53 and its transcriptional targets, p21 and PUMA, in HCT116 cells. Docking poses and residues involved in the inhibition of p53-MDM2/X interactions were predicted by docking studies.
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Affiliation(s)
- Joana Moreira
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal.,CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões, 4450-208, Matosinhos, Portugal
| | - Joana Almeida
- LAQV/REQUIMTE, Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Joana B Loureiro
- LAQV/REQUIMTE, Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Helena Ramos
- LAQV/REQUIMTE, Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Andreia Palmeira
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal.,CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões, 4450-208, Matosinhos, Portugal
| | - Madalena M Pinto
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal.,CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões, 4450-208, Matosinhos, Portugal
| | - Lucília Saraiva
- LAQV/REQUIMTE, Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Honorina Cidade
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal.,CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Terminal de Cruzeiros do Porto de Leixões, 4450-208, Matosinhos, Portugal
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24
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Mondal SK, Mukhoty S, Kundu H, Ghosh S, Sen MK, Das S, Brogi S. In silico analysis of RNA-dependent RNA polymerase of the SARS-CoV-2 and therapeutic potential of existing antiviral drugs. Comput Biol Med 2021; 135:104591. [PMID: 34216889 PMCID: PMC8220294 DOI: 10.1016/j.compbiomed.2021.104591] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 06/17/2021] [Accepted: 06/17/2021] [Indexed: 01/18/2023]
Abstract
The continued sustained threat of the SARS-CoV-2 virus world-wide, urgently calls for far-reaching effective therapeutic strategies for treating this emerging infection. Accordingly, this study explores mode of action and therapeutic potential of existing antiviral drugs. Multiple sequence alignment and phylogenetic analyses indicate that the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 was mutable and similar to bat coronavirus RaTG13. Successive interactions between RdRp (nsp12 alone or in complex with cofactors nsp7-8) and viral RNA demonstrated that the binding affinity values remained the same, but the sites of interaction of RdRp (highly conserved for homologous sequences from different organisms) were altered in the presence of selected antiviral drugs such as Remdesivir, and Sofosbuvir. The antiviral drug Sofosbuvir reduced the number of hydrogen bonds formed between RdRp and RNA. Remdesivir bound more tightly to viral RNA than viral RdRp alone or the nsp12-7-8 hexadecameric complex, resulting in a significant number of hydrogen bonds being formed in the uracil-rich region. The interaction between nsp12-7-8 complex and RNA was mediated by specific interaction sites of nsp7-8. Therefore, the conserved nature of RdRp interaction sites, and alterations due to drug intervention indicate the therapeutic potential of the selected drugs. In this article, we provide additional focus on the interacting amino acids of the nsp7-8 complex and highlight crucial regions that could be targeted for precluding a correct recognition of subunits involved in the hexadecameric assembly, to rationally design molecules endowed with a significant antiviral profile.
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Affiliation(s)
- Sunil Kanti Mondal
- Department of Biotechnology, The University of Burdwan, Burdwan, 713104, West Bengal, India.
| | - Samyabrata Mukhoty
- Department of Biotechnology, The University of Burdwan, Burdwan, 713104, West Bengal, India
| | - Himangsu Kundu
- Department of Biotechnology, The University of Burdwan, Burdwan, 713104, West Bengal, India
| | - Subhajit Ghosh
- Department of Biotechnology, The University of Burdwan, Burdwan, 713104, West Bengal, India
| | - Madhab Kumar Sen
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Suvankar Das
- Department of Genetics, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, India
| | - Simone Brogi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126, Pisa, Italy.
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25
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Bolz SN, Adasme MF, Schroeder M. Toward an Understanding of Pan-Assay Interference Compounds and Promiscuity: A Structural Perspective on Binding Modes. J Chem Inf Model 2021; 61:2248-2262. [PMID: 33899463 DOI: 10.1021/acs.jcim.0c01227] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Pan-assay interference compounds (PAINS) are promiscuous compound classes that produce false positive hits in high-throughput screenings. Yet, the mechanisms of PAINS activity are poorly understood. Although PAINS are often associated with protein reactivity, several recent studies have shown that they also mediate noncovalent interactions. Aiming at a deep understanding of PAINS promiscuity, we performed an analysis of the Protein Data Bank to characterize the binding modes of PAINS. We explored the binding mode conservation of 34 PAINS classes present in 871 ligands and among 517 protein targets. The two major findings of this work are the following: First, different PAINS classes exhibit different levels of binding mode conservation. Our novel classification of PAINS based on binding mode similarity enables a rational assessment of PAINS from a structural perspective. Second, PAINS classes with variable binding modes can bind with high affinity. The evaluation of noncovalent binding modes of PAINS-like compounds sheds light on the mechanisms of promiscuous binding. Our findings could facilitate the decisions on how to deal with PAINS and help scientists to understand why PAINS produce hits in their screenings.
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Affiliation(s)
- Sarah Naomi Bolz
- Biotechnology Center (BIOTEC), Technische Universität Dresden, 01307 Dresden, Germany
| | - Melissa F Adasme
- Biotechnology Center (BIOTEC), Technische Universität Dresden, 01307 Dresden, Germany
| | - Michael Schroeder
- Biotechnology Center (BIOTEC), Technische Universität Dresden, 01307 Dresden, Germany
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26
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Nayarisseri A, Khandelwal R, Tanwar P, Madhavi M, Sharma D, Thakur G, Speck-Planche A, Singh SK. Artificial Intelligence, Big Data and Machine Learning Approaches in Precision Medicine & Drug Discovery. Curr Drug Targets 2021; 22:631-655. [PMID: 33397265 DOI: 10.2174/1389450122999210104205732] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 08/21/2020] [Accepted: 09/14/2020] [Indexed: 11/22/2022]
Abstract
Artificial Intelligence revolutionizes the drug development process that can quickly identify potential biologically active compounds from millions of candidate within a short period. The present review is an overview based on some applications of Machine Learning based tools, such as GOLD, Deep PVP, LIB SVM, etc. and the algorithms involved such as support vector machine (SVM), random forest (RF), decision tree and Artificial Neural Network (ANN), etc. at various stages of drug designing and development. These techniques can be employed in SNP discoveries, drug repurposing, ligand-based drug design (LBDD), Ligand-based Virtual Screening (LBVS) and Structure- based Virtual Screening (SBVS), Lead identification, quantitative structure-activity relationship (QSAR) modeling, and ADMET analysis. It is demonstrated that SVM exhibited better performance in indicating that the classification model will have great applications on human intestinal absorption (HIA) predictions. Successful cases have been reported which demonstrate the efficiency of SVM and RF models in identifying JFD00950 as a novel compound targeting against a colon cancer cell line, DLD-1, by inhibition of FEN1 cytotoxic and cleavage activity. Furthermore, a QSAR model was also used to predict flavonoid inhibitory effects on AR activity as a potent treatment for diabetes mellitus (DM), using ANN. Hence, in the era of big data, ML approaches have been evolved as a powerful and efficient way to deal with the huge amounts of generated data from modern drug discovery to model small-molecule drugs, gene biomarkers and identifying the novel drug targets for various diseases.
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Affiliation(s)
- Anuraj Nayarisseri
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Ravina Khandelwal
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Poonam Tanwar
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Maddala Madhavi
- Department of Zoology, Nizam College, Osmania University, Hyderabad - 500001, Telangana State, India
| | - Diksha Sharma
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Garima Thakur
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Alejandro Speck-Planche
- Programa Institucional de Fomento a la Investigacion, Desarrollo e Innovacion, Universidad Tecnologica Metropolitana, Ignacio Valdivieso 2409, P.O. 8940577, San Joaquin, Santiago, Chile
| | - Sanjeev Kumar Singh
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630003, Tamil Nadu, India
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27
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Discovery of Potential Inhibitors for RNA-Dependent RNA Polymerase of Norovirus: Virtual Screening, and Molecular Dynamics. Int J Mol Sci 2020; 22:ijms22010171. [PMID: 33375298 PMCID: PMC7795727 DOI: 10.3390/ijms22010171] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 11/26/2020] [Accepted: 11/26/2020] [Indexed: 01/16/2023] Open
Abstract
Noroviruses are non-enveloped viruses with a positive-sense single-stranded RNA (ssRNA) genome belonging to the genus Norovirus, from the family Caliciviridae, which are accountable for acute gastroenteritis in humans. The Norovirus genus is subdivided into seven genogroups, i.e., (GI-GVII); among these, the genogroup II and genotype 4 (GII.4) strains caused global outbreaks of human norovirus (HuNov) disease. The viral genome comprises three open reading frames (ORFs). ORF1 encodes the nonstructural polyprotein that is cleaved into six nonstructural proteins, which include 3C-like cysteine protease (3CLpro) and a viral RNA-dependent RNA polymerase. ORF2 and ORF3 encode the proteins VP1 and VP2. The RNA-dependent RNA polymerase (RdRp) from noroviruses is one of the multipurpose enzymes of RNA viruses vital for replicating and transcribing the viral genome, making the virally encoded enzyme one of the critical targets for the development of novel anti-norovirus agents. In the quest for a new antiviral agent that could combat HuNov, high throughput virtual screening (HTVS), combined with e-pharmacophore screening, was applied to screen compounds from the PubChem database. CMX521 molecule was selected as a prototype for a similarity search in the PubChem online database. Molecular dynamics simulations were employed to identify different compounds that may inhibit HuNov. The results predicted that compound CID-57930781 and CID-44396095 formed stable complexes with MNV-RdRp within 50 ns; hence, they may signify as promising human norovirus inhibitors.
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da Silva ER, Come JAADSS, Brogi S, Calderone V, Chemi G, Campiani G, Oliveira TMFDS, Pham TN, Pudlo M, Girard C, Maquiaveli CDC. Cinnamides Target Leishmania amazonensis Arginase Selectively. MOLECULES (BASEL, SWITZERLAND) 2020; 25:molecules25225271. [PMID: 33198198 PMCID: PMC7696938 DOI: 10.3390/molecules25225271] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/02/2020] [Accepted: 11/06/2020] [Indexed: 11/20/2022]
Abstract
Caffeic acid and related natural compounds were previously described as Leishmania amazonensis arginase (L-ARG) inhibitors, and against the whole parasite in vitro. In this study, we tested cinnamides that were previously synthesized to target human arginase. The compound caffeic acid phenethyl amide (CAPA), a weak inhibitor of human arginase (IC50 = 60.3 ± 7.8 μM) was found to have 9-fold more potency against L-ARG (IC50 = 6.9 ± 0.7 μM). The other compounds that did not inhibit human arginase were characterized as L-ARG, showing an IC50 between 1.3–17.8 μM, and where the most active was compound 15 (IC50 = 1.3 ± 0.1 μM). All compounds were also tested against L. amazonensis promastigotes, and only the compound CAPA showed an inhibitory activity (IC50 = 80 μM). In addition, in an attempt to gain an insight into the mechanism of competitive L-ARG inhibitors, and their selectivity over mammalian enzymes, we performed an extensive computational investigation, to provide the basis for the selective inhibition of L-ARG for this series of compounds. In conclusion, our results indicated that the compounds based on cinnamoyl or 3,4-hydroxy cinnamoyl moiety could be a promising starting point for the design of potential antileishmanial drugs based on selective L-ARG inhibitors.
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Affiliation(s)
- Edson Roberto da Silva
- Laboratório de Farmacologia e Bioquímica (LFBq), Departamento de Medicina Veterinária, Universidade de São Paulo Faculdade de Zootecnia e Engenharia de Alimentos, Pirassununga, SP 13635-900, Brazil; (J.A.A.d.S.S.C.); (T.M.F.d.S.O.)
- Correspondence: (E.R.d.S.); (S.B.); (C.G.); (C.d.C.M.)
| | - Júlio Abel Alfredo dos Santos Simone Come
- Laboratório de Farmacologia e Bioquímica (LFBq), Departamento de Medicina Veterinária, Universidade de São Paulo Faculdade de Zootecnia e Engenharia de Alimentos, Pirassununga, SP 13635-900, Brazil; (J.A.A.d.S.S.C.); (T.M.F.d.S.O.)
- Departamento de Pré-Clínicas, Universidade Eduardo Mondlane, Faculdade de Veterinária, Av. de Moçambique, Km 1.5, Maputo CP 257, Mozambique
| | - Simone Brogi
- Department of Pharmacy, University of Pisa, via Bonanno 6, 56126 Pisa, Italy;
- Correspondence: (E.R.d.S.); (S.B.); (C.G.); (C.d.C.M.)
| | - Vincenzo Calderone
- Department of Pharmacy, University of Pisa, via Bonanno 6, 56126 Pisa, Italy;
| | - Giulia Chemi
- Department of Biotechnology, Chemistry, and Pharmacy, DoE Department of Excellence 2018–2022 Università degli Studi di Siena via Aldo Moro 2, 53100 Siena, Italy; (G.C.); (G.C.)
| | - Giuseppe Campiani
- Department of Biotechnology, Chemistry, and Pharmacy, DoE Department of Excellence 2018–2022 Università degli Studi di Siena via Aldo Moro 2, 53100 Siena, Italy; (G.C.); (G.C.)
| | - Trícia Maria Ferrreira de Sousa Oliveira
- Laboratório de Farmacologia e Bioquímica (LFBq), Departamento de Medicina Veterinária, Universidade de São Paulo Faculdade de Zootecnia e Engenharia de Alimentos, Pirassununga, SP 13635-900, Brazil; (J.A.A.d.S.S.C.); (T.M.F.d.S.O.)
| | - Thanh-Nhat Pham
- PEPITE EA4267, University Bourgogne Franche-Comté, F-25000 Besançon, France; (T.-N.P.); (M.P.)
| | - Marc Pudlo
- PEPITE EA4267, University Bourgogne Franche-Comté, F-25000 Besançon, France; (T.-N.P.); (M.P.)
| | - Corine Girard
- PEPITE EA4267, University Bourgogne Franche-Comté, F-25000 Besançon, France; (T.-N.P.); (M.P.)
- Correspondence: (E.R.d.S.); (S.B.); (C.G.); (C.d.C.M.)
| | - Claudia do Carmo Maquiaveli
- Laboratório de Farmacologia e Bioquímica (LFBq), Departamento de Medicina Veterinária, Universidade de São Paulo Faculdade de Zootecnia e Engenharia de Alimentos, Pirassununga, SP 13635-900, Brazil; (J.A.A.d.S.S.C.); (T.M.F.d.S.O.)
- Correspondence: (E.R.d.S.); (S.B.); (C.G.); (C.d.C.M.)
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Siniprasad P, Nair B, Balasubramaniam V, Sadanandan P, Namboori PK, Nath LR. Evaluation of Kaempferol as AKT Dependent mTOR Regulator via Targeting FKBP-12 in Hepatocellular Carcinoma: An In silico Approach. LETT DRUG DES DISCOV 2020. [DOI: 10.2174/1570180817999200623115703] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Background:
Hepatocellular carcinomas (HCCs) are inherently chemotherapy-resistant
tumors with about 30-50% activation of PI3K/Akt/mTOR pathway, and this pathway is not aberrant
in normal cells. Therefore, targeting the PI3K/Akt/mTOR pathway has become a promising strategy
in drug designing to combat liver cancer. Recently, many studies with phytochemicals suggest few classes
of compounds, especially flavonoids, to be useful in down-regulating the PI3K/Akt/mTOR pathway corresponding
to HCC. In the present study, an attempt is made to explore flavonoids, from which the best
mTORC1 inhibitor against hepatocellular carcinoma is selected using computational molecular modeling.
Methods:
In the present study, we performed a virtual screening method with phytochemicals of
flavonoid category. To ensure proper bioavailability and druggability, pharmacokinetic and interaction
parameters have been used to screen the molecules. The target protein molecules have been selected
from the RCSB. The interaction studies have been conducted using Biovia Discovery Studio
client version 17.2.0.1.16347 and the pharmacokinetic predictions have been made through ADMET
SAR. The responsiveness towards the regulation of the mTOR pathway varies from person to person,
demanding a pharmacogenomic approach in the analysis. The genetic variants (Single Nucleotide
Variants-SNVs) corresponding to the mutations have been identified.
Results and Discussion:
The study identified phytoconstituents with better interaction with receptor
FKBP12, a Rapamycin binding domain which is the target of Rapamycin and its analogues for
mTORC1 inhibition in HCC. Another protein, ‘AKT serine/threonine-protein kinase’ has been identified,
which is associated with activation of mTORC1. The molecular interaction studies (docking
studies) and ADMET (absorption, distribution, metabolism, excretion and toxicity) analysis were
used to identify the affinity between selected phytoconstituents as mTORC1 inhibitor against Hepatocellular
carcinoma. The docking studies support Kaempferol to be a potential ligand with docking
score values of 33.4 (3CQU-3D structure of AKT1)] and 27.3 (2FAP-3D structure of FRB domain
of mTOR) respectively as compared to that of standard drug Everolimus with 24.4 (3CQU-3D structure
of AKT1) and 20.1 (2FAP-3D structure of FRB domain of mTOR) respectively. Docking studies
along with ADMET results show that Kaempferol has favorable drug likeliness properties and
binds to the same active site (site1) of the targeted proteins (3CQU-3D structure of AKT1) and
(2FAP-3D structure of FRB domain of mTOR) where the standard drug Everolimus is known to
bind.
Conclusion:
The study exhibited that Kaempferol had a better binding affinity towards the receptor
FKBP12, a Rapamycin Binding Domain and AKT serine/threonine-protein kinase resulting in its
better efficacy in the mTORC1 inhibition as when compared with standard drug Everolimus against
HCC. To the best of our knowledge, no studies have been reported on Kaempferol as mTORC1 inhibitor
against Hepatocellular carcinoma.
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Affiliation(s)
- Pooja Siniprasad
- Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Ponekkara P.O., Kochi, Kerala 682041, India
| | - Bhagyalakshmi Nair
- Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Ponekkara P.O., Kochi, Kerala 682041, India
| | - Vaisali Balasubramaniam
- Computational Chemistry Group (CCG), Computational Engineering and Networking, Amrita Vishwa Vidyapeetham, Amritanagar, Coimbatore-641112, India
| | - Prashanth Sadanandan
- Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Ponekkara P.O., Kochi, Kerala 682041, India
| | - Puliyapally Krishnan Namboori
- Computational Chemistry Group (CCG), Computational Engineering and Networking, Amrita Vishwa Vidyapeetham, Amritanagar, Coimbatore-641112, India
| | - Lekshmi Reghu Nath
- Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Ponekkara P.O., Kochi, Kerala 682041, India
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Computer-Driven Development of an in Silico Tool for Finding Selective Histone Deacetylase 1 Inhibitors. Molecules 2020; 25:molecules25081952. [PMID: 32331470 PMCID: PMC7221830 DOI: 10.3390/molecules25081952] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 04/18/2020] [Accepted: 04/20/2020] [Indexed: 12/19/2022] Open
Abstract
Histone deacetylases (HDACs) are a class of epigenetic modulators overexpressed in numerous types of cancers. Consequently, HDAC inhibitors (HDACIs) have emerged as promising antineoplastic agents. Unfortunately, the most developed HDACIs suffer from poor selectivity towards a specific isoform, limiting their clinical applicability. Among the isoforms, HDAC1 represents a crucial target for designing selective HDACIs, being aberrantly expressed in several malignancies. Accordingly, the development of a predictive in silico tool employing a large set of HDACIs (aminophenylbenzamide derivatives) is herein presented for the first time. Software Phase was used to derive a 3D-QSAR model, employing as alignment rule a common-features pharmacophore built on 20 highly active/selective HDAC1 inhibitors. The 3D-QSAR model was generated using 370 benzamide-based HDACIs, which yielded an excellent correlation coefficient value (R2 = 0.958) and a satisfactory predictive power (Q2 = 0.822; Q2F3 = 0.894). The model was validated (r2ext_ts = 0.794) using an external test set (113 compounds not used for generating the model), and by employing a decoys set and the receiver-operating characteristic (ROC) curve analysis, evaluating the Güner-Henry score (GH) and the enrichment factor (EF). The results confirmed a satisfactory predictive power of the 3D-QSAR model. This latter represents a useful filtering tool for screening large chemical databases, finding novel derivatives with improved HDAC1 inhibitory activity.
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Structure-activity relationships study of isothiocyanates for H 2S releasing properties: 3-Pyridyl-isothiocyanate as a new promising cardioprotective agent. J Adv Res 2020; 27:41-53. [PMID: 33318865 PMCID: PMC7728584 DOI: 10.1016/j.jare.2020.02.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/27/2020] [Accepted: 02/29/2020] [Indexed: 12/13/2022] Open
Abstract
Introduction The gasotransmitter hydrogen sulphide (H2S), an endogenous ubiquitous signalling molecule, is known for its beneficial effects on different mammalian systems. H2S exhibits cardioprotective activity against ischemia/reperfusion (I/R) or hypoxic injury. Methods A library of forty-five isothiocyanates, selected for their different chemical properties, has been evaluated for its hydrogen sulfide (H2S) releasing capacity. The obtained results allowed to correlate several factors such as steric hindrance, electronic effects and position of the substituents to the observed H2S production. Moreover, the chemical-physical profiles of the selected compounds have been studied by an in silico approach and from a combination of the obtained results, 3-pyridyl-isothiocyanate (25) has been selected as the most promising one. A detailed pharmacological characterization of its cardioprotective action has been performed. Results The results herein obtained strongly indicate 3-pyridyl-isothiocyanate (25) as a suitable pharmacological option in anti-ischemic therapy. The cardioprotective effects of compound 25 were tested in vivo and found to exhibit a positive effect. Conclusion Results strongly suggest that isothiocyanate-based H2S-releasing drugs, such as compound 25, can trigger a ‘‘pharmacological pre-conditioning” and could represent a suitable pharmacological option in antiischemic therapy.
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Pallante L, Rocca A, Klejborowska G, Huczynski A, Grasso G, Tuszynski JA, Deriu MA. In silico Investigations of the Mode of Action of Novel Colchicine Derivatives Targeting β-Tubulin Isotypes: A Search for a Selective and Specific β-III Tubulin Ligand. Front Chem 2020; 8:108. [PMID: 32154219 PMCID: PMC7047339 DOI: 10.3389/fchem.2020.00108] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 02/04/2020] [Indexed: 01/04/2023] Open
Abstract
The cardinal role of microtubules in cell mitosis makes them interesting drug targets for many pharmacological treatments, including those against cancer. Moreover, different expression patterns between cell types for several tubulin isotypes represent a great opportunity to improve the selectivity and specificity of the employed drugs and to design novel compounds with higher activity only on cells of interest. In this context, tubulin isotype βIII represents an excellent target for anti-tumoral therapies since it is overexpressed in most cancer cells and correlated with drug resistance. Colchicine is a well-known antimitotic agent, which is able to bind the tubulin dimer and to halt the mitotic process. However, it shows high toxicity also on normal cells and it is not specific for isotype βIII. In this context, the search for colchicine derivatives is a matter of great importance in cancer research. In this study, homology modeling techniques, molecular docking, and molecular dynamics simulations have been employed to characterize the interaction between 55 new promising colchicine derivatives and tubulin isotype βIII. These compounds were screened and ranked based on their binding affinity and conformational stability in the colchicine binding site of tubulin βIII. Results from this study point the attention on an amide of 4-chlorine thiocolchicine. This colchicine-derivative is characterized by a unique mode of interaction with tubulin, compared to all other compounds considered, which is primarily characterized by the involvement of the α-T5 loop, a key player in the colchicine binding site. Information provided by the present study may be particularly important in the rational design of colchicine-derivatives targeting drug resistant cancer phenotypes.
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Affiliation(s)
- Lorenzo Pallante
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Antonio Rocca
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | | | - Adam Huczynski
- Department of Chemistry, Adam Mickiewicz University, Poznań, Poland
| | - Gianvito Grasso
- Dalle Molle Institute for Artificial Intelligence (IDSIA), University of Applied Sciences of Southern Switzerland (SUPSI), University of Italian Switzerland (USI), Manno, Switzerland
| | - Jack A Tuszynski
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy.,Department of Oncology, University of Alberta, Edmonton, AB, Canada
| | - Marco A Deriu
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
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Brogi S, Sirous H, Calderone V, Chemi G. Amyloid β fibril disruption by oleuropein aglycone: long-time molecular dynamics simulation to gain insight into the mechanism of action of this polyphenol from extra virgin olive oil. Food Funct 2020; 11:8122-8132. [DOI: 10.1039/d0fo01511c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Insight into the mechanism of action of oleuropein aglycone as a potent anti-amyloidogenic agent.
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Affiliation(s)
- Simone Brogi
- Department of Pharmacy
- University of Pisa
- 56126 Pisa
- Italy
| | - Hajar Sirous
- Bioinformatics Research Center
- School of Pharmacy and Pharmaceutical Sciences
- Isfahan University of Medical Sciences
- 81746-73461 Isfahan
- Iran
| | | | - Giulia Chemi
- Wellcome Centre for Anti-Infectives Research
- Drug Discovery Unit
- Division of Biological Chemistry and Drug Discovery
- University of Dundee
- DD1 5EH Dundee
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34
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Liu X, Tian W, Cheng J, Li D, Liu T, Zhang L. Microsecond molecular dynamics simulations reveal the allosteric regulatory mechanism of p53 R249S mutation in p53-associated liver cancer. Comput Biol Chem 2019; 84:107194. [PMID: 31881526 DOI: 10.1016/j.compbiolchem.2019.107194] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 12/10/2019] [Accepted: 12/11/2019] [Indexed: 02/08/2023]
Abstract
The tumor suppressor p53, a transcription factor, plays a critical role in many cellular processes, including DNA repair and apoptosis and cell cycle arrest. Missense mutations in the p53 have closely related to human cancer. R249S mutation at the p53 core DNA binding domain (DBD) is frequently observed in hepatocellular carcinoma. This mutation is away from the p53 DBD-DNA binding interface. However, how the R249S mutation causes the structural changes of p53 DBD that lead to weak the binding of p53 mutant to DNA has not been clearly understood. Here, microsecond-scale molecular dynamics (MD) simulations of p53 DBD in the wild type (WT) and R249S mutated states in the absence of DNA binding were performed to explore the effect of the R249S mutation on the conformational dynamics of p53 DBD. The R249S mutation does not cause the global conformational changes, and it only affects the local domains at the mutation site and the DNA binding interface, particularly at the S1-S2 turn. The allosteric effects of the S1-S2 turn induced by the R249S mutation lead to the extension of the S1-S2 turn into the β-strands, which in turn interferes with the binding of DNA at the major groove. The results can help decipher the allosteric regulatory mechanism by which the R249S mutation of p53 DBD affects the p53 DBD-DNA interactions.
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Affiliation(s)
- Xianxian Liu
- Department of Infectious Diseases, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Wenchao Tian
- Pediatric Surgery, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Jinying Cheng
- Department of Infectious Diseases, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Dongmei Li
- Department of Infectious Diseases, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Tonggang Liu
- Department of Infectious Diseases, Binzhou Medical University Hospital, Binzhou, Shandong, China.
| | - Liguo Zhang
- Department of Infectious Diseases, Binzhou Medical University Hospital, Binzhou, Shandong, China.
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