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Bhowmik P, Baezid HM, Arabi II. Assessment of antidiabetic activity of three Phenylspirodrimanes from fungus Stachybotrys chartarum MUT 3308 by ADME, QSAR, molecular docking and molecular dynamics simulation studies against protein tyrosine phosphatase 1B (PTP1B). J Biomol Struct Dyn 2023:1-15. [PMID: 37698508 DOI: 10.1080/07391102.2023.2256410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 08/24/2023] [Indexed: 09/13/2023]
Abstract
Phenylspirodrimanes (PSD) are the sesquiterpene quinone type meroterpenoids found in nature. PSDs are found to exhibit inhibitory activity against immunocomplex diseases, and tyrosine kinase receptors. Three of the different PSDs C1, C2, and C3 that have been reported to be isolated from the sponge-associated fungus Stachybotrys chartarum MUT 3308 are selected for studying their possible inhibitory effect against type 2 diabetes mellitus. Mechanistically, blocking protein tyrosine phosphatase 1B (PTP1B) helps to reduce the insulin resistance induction caused by the high expression of PTP1B. The QSAR, ADME, toxicity (T) study was carried out to predict the pharmacokinetic properties and the biological activities of the PSDs. PASS prediction web tool was used to find and select the target proteins 1NNY, and 2HNP. According to the molecular docking simulations, C1 and C2 showed better binding affinity of -8.5 kcal/mol, and -8.1 kcal/mol respectively against 1NNY compared to the control ligand. RMSD, RMSF, Rg, and SASA analysis revealed that both C1, and C2 showed better stability, minor conformational changes, and minor fluctuation upon binding to PTP1B. Protein contact analysis was carried out to validate the residues that are in contact with the ligands according to molecular docking studies. Overall, C1, and C2 could be proposed as novel natural hits to be developed and small modifications of these PSDs could result in inducing the binding affinity significantly, although experimental validation is required for further evaluation of the work.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Prasenjit Bhowmik
- Department of Chemistry-BMC, Biochemistry, Disciplinary Domain of Science and Technology, Uppsala University, Uppsala, Sweden
- Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
- Department of Textile Engineering, Green University of Bangladesh, Narayanganj, Bangladesh
| | - Hossain Mohammad Baezid
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong, Bangladesh
| | - Ishmam Ibnul Arabi
- Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
- Department of Textile Engineering, Green University of Bangladesh, Narayanganj, Bangladesh
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Dey SK, Saini M, Dhembla C, Bhatt S, Rajesh AS, Anand V, Das HK, Kundu S. Suramin, penciclovir, and anidulafungin exhibit potential in the treatment of COVID-19 via binding to nsp12 of SARS-CoV-2. J Biomol Struct Dyn 2022; 40:14067-14083. [PMID: 34784490 DOI: 10.1080/07391102.2021.2000498] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
COVID-19, for which no confirmed therapeutic agents are available, has claimed over 48,14,000 lives globally. A feasible and quicker method to resolve this problem may be 'drug repositioning'. We investigated selected FDA and WHO-EML approved drugs based on their previously promising potential as antivirals, antibacterials or antifungals. These drugs were docked onto the nsp12 protein, which reigns the RNA-dependent RNA polymerase activity of SARS-CoV-2, a key therapeutic target for coronaviruses. Docked complexes were reevaluated using MM-GBSA analysis and the top three inhibitor-protein complexes were subjected to 100 ns long molecular dynamics simulation followed by another round of MM-GBSA analysis. The RMSF plots, binding energies and the mode of physicochemical interaction of the active site of the protein with the drugs were evaluated. Suramin, Penciclovir, and Anidulafungin were found to bind to nsp12 with similar binding energies as that of Remdesivir, which has been used as a therapy for COVID-19. In addition, recent experimental evidences indicate that these drugs exhibit antiviral efficacy against SARS-CoV-2. Such evidence, along with the significant and varied physical interactions of these drugs with the key viral enzyme outlined in this investigation, indicates that they might have a prospective therapeutic potential in the treatment of COVID-19 as monotherapy or combination therapy with Remdesivir.
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Affiliation(s)
- Sanjay Kumar Dey
- Center for Advanced Biotechnology and Medicine, Rutgers University, New Brunswick, New Jersey, USA.,Department of Biochemistry, University of Delhi South Campus, New Delhi, India.,Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Manisha Saini
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Chetna Dhembla
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Shruti Bhatt
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - A Sai Rajesh
- Department of Biosciences and Biotechnology, Fakir Mohan University, Odisha, India
| | - Varnita Anand
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | | | - Suman Kundu
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
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Mohsin NUA, Aslam S, Ahmad M, Irfan M, Al-Hussain SA, Zaki MEA. Cyclooxygenase-2 (COX-2) as a Target of Anticancer Agents: A Review of Novel Synthesized Scaffolds Having Anticancer and COX-2 Inhibitory Potentialities. Pharmaceuticals (Basel) 2022; 15:ph15121471. [PMID: 36558921 PMCID: PMC9783503 DOI: 10.3390/ph15121471] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/19/2022] [Accepted: 11/21/2022] [Indexed: 11/29/2022] Open
Abstract
Cancer is a serious threat to human beings and is the second-largest cause of death all over the globe. Chemotherapy is one of the most common treatments for cancer; however, drug resistance and severe adverse effects are major problems associated with anticancer therapy. New compounds with multi-target inhibitory properties are targeted to surmount these challenges. Cyclooxygenase-2 (COX-2) is overexpressed in cancers of the pancreas, breast, colorectal, stomach, and lung carcinoma. Therefore, COX-2 is considered a significant target for the synthesis of new anticancer agents. This review discusses the biological activity of recently prepared dual anticancer and COX-2 inhibitory agents. The most important intermolecular interactions with the COX-2 enzyme have also been presented. Analysis of these agents in the active area of the COX-2 enzyme could guide the introduction of new lead compounds with extreme selectivity and minor side effects.
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Affiliation(s)
- Noor ul Amin Mohsin
- Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Government College University, Faisalabad 38000, Pakistan
| | - Sana Aslam
- Department of Chemistry, Government College Women University, Faisalabad 38000, Pakistan
| | - Matloob Ahmad
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan
- Correspondence: (M.A.); (M.E.A.Z.)
| | - Muhammad Irfan
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Government College University, Faisalabad 38000, Pakistan
| | - Sami A. Al-Hussain
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia
| | - Magdi E. A. Zaki
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia
- Correspondence: (M.A.); (M.E.A.Z.)
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Khavani M, Mehranfar A, Vahid H. Application of amino acid ionic liquids for increasing the stability of DNA in long term storage. J Biomol Struct Dyn 2022:1-15. [PMID: 35467487 DOI: 10.1080/07391102.2022.2067239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The structural stability of DNA is important because of its biological activity. DNAs due to their inherent chemical properties are not stable in an aqueous solution, therefore, a long period of storage of DNA at the ambient condition in bioscience is of importance. Ionic liquids (ILs) as interesting alternatives compared to organic solvents and water due to their considerable properties can be used as new agents to increase the stability of DNA for a long period of storage. In this article, molecular dynamics (MD) simulations and quantum chemistry calculations were applied to investigate the effects of amino acid ionic liquids ([BMIM][Ala], [BMIM][Gly], [BMIM][Val], [BMIM][Pro] and [BMIM][Leu]) on the dynamical behavior and the structural stability of calf thymus DNA. Based on the obtained MD results ILs enter into the solvation shell of the DNA and push away the water molecules from the DNA surface. Structural analysis shows that [BMIM]+ cations can occupy the DNA minor groove without disturbing the double-helical structure of DNA. ILs due to strong electrostatic and van der Waals (vdW) interactions with the DNA structure contribute to the stability of the double-helical structure. Quantum chemistry calculations indicate that the interactions between the [BMIM]+ cation and DNA structure has an electrostatic character. Moreover, this cation forms a more stable complex with the CGCG region of the DNA in comparison with AATT base pairs. Overall, the results of this study can provide new insight into the application of ILs for maintaining DNA stability during long-term storage.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohammad Khavani
- Department of Chemistry and Materials Science, School of Chemical Engineering, Aalto University, Aalto, Finland.,Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, Berkeley, California, USA
| | - Aliyeh Mehranfar
- Department of Chemistry and Materials Science, School of Chemical Engineering, Aalto University, Aalto, Finland
| | - Hossein Vahid
- Department of Chemistry and Materials Science, School of Chemical Engineering, Aalto University, Aalto, Finland.,Department of Applied Physics, Aalto University, Aalto, Finland
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Inhibitory Mechanisms of Lusianthridin on Human Platelet Aggregation. Int J Mol Sci 2021; 22:ijms22136846. [PMID: 34202163 PMCID: PMC8267677 DOI: 10.3390/ijms22136846] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/16/2021] [Accepted: 06/21/2021] [Indexed: 12/25/2022] Open
Abstract
Lusianthridin is a phenanthrene derivative isolated from Dendrobium venustum. Some phenanthrene compounds have antiplatelet aggregation activities via undefined pathways. This study aims to determine the inhibitory effects and potential mechanisms of lusianthridin on platelet aggregation. The results indicated that lusianthridin inhibited arachidonic acid, collagen, and adenosine diphosphate (ADP)-stimulated platelet aggregation (IC50 of 0.02 ± 0.001 mM, 0.14 ± 0.018 mM, and 0.22 ± 0.046 mM, respectively). Lusianthridin also increased the delaying time of arachidonic acid-stimulated and the lag time of collagen-stimulated and showed a more selective effect on the secondary wave of ADP-stimulated aggregations. Molecular docking studies revealed that lusianthridin bound to the entrance site of the cyclooxygenase-1 (COX-1) enzyme and probably the active region of the cyclooxygenase-2 (COX-2) enzyme. In addition, lusianthridin showed inhibitory effects on both COX-1 and COX-2 enzymatic activities (IC50 value of 10.81 ± 1.12 µM and 0.17 ± 1.62 µM, respectively). Furthermore, lusianthridin significantly inhibited ADP-induced suppression of cAMP formation in platelets at 0.4 mM concentration (p < 0.05). These findings suggested that possible mechanisms of lusianthridin on the antiplatelet effects might act via arachidonic acid-thromboxane and adenylate cyclase pathways.
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Mohammad AT, Abbas WR. Liquid crystal behavior, photoluminescence and gas sensing: A new series of ionic liquid crystal imidazole and benzoimidazole bearing chalcone groups, synthesis and characterization. RSC Adv 2021; 11:38444-38456. [PMID: 35493216 PMCID: PMC9044318 DOI: 10.1039/d1ra07731g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 11/11/2021] [Indexed: 11/21/2022] Open
Abstract
Four new series of chalcones containing imidazole bromonium and benzimidazole bromonium salts with spacer alkyl chains (Cn, n = 2 and 4) were synthesized and the chemical structure, thermal behavior, photoluminescence and gas sensing were characterized by several technical methods. The studies have indicated similar mesomorphic properties of the synthesized compounds, dependent on the terminal alkyl-chain and lengths of the alkoxy-spacer. Almost compounds with shorter alky chains, 4a–4e, 5a–5c, 6a–6c and 7a–7d, did not show liquid crystal properties, while the results of other compounds confirm the existence of smectic A in cooling and heating cycles. Photoluminescence of compounds 5a–5i and 7a–7i was also studied. The emission in the blue region reveals that the material has blue light emission properties. Sensing behavior of compounds 4i and 5i was investigated for NH3 and NO2 gases. The sensors exhibited high sensitivity toward NH3, while sensitivity toward the oxidizing gas NO2 is lower. Four new series of chalcones containing imidazole bromonium and benzimidazole bromonium salts with spacer alkyl chains (Cn, n = 2 and 4) were synthesized and their chemical structure, thermal behavior, photoluminescence and gas sensing ability were characterized.![]()
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Affiliation(s)
| | - Wahaj Raed Abbas
- Chemistry Department, College of Science, University of Anbar, Ramadi, Iraq
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Celik S, Yilmaz G, Ozel AE, Akyuz S. Structural and spectral analysis of anticancer active cyclo(Ala-His) dipeptide. J Biomol Struct Dyn 2020; 40:660-672. [PMID: 32909514 DOI: 10.1080/07391102.2020.1817150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The theoretically possible most stable conformation of the cyclic dipeptide, which has a significant anticancer activity, was examined by conformational analysis method and then by DFT calculations. With DFT calculations, cyclo(Ala-His) dipeptide was found to be more stable in boat form than in planar conformation. Moreover, conformations of the dimeric forms of the title molecule were investigated. The dimeric forms of the cyclo(Ala-His) dipeptide were created by combining two identical cyclo(Ala-His) monomers, in lowest energy configuration and as a result three energetically possible dimeric structures were obtained. The solid phase FTIR and Raman spectra of cyclo(Ala-His) have been recorded. The spectra were interpreted with the aid of quantum chemical calculations based on density functional theory, using B3LYP and wb97xd methods with 6-311++G(d,p) basis set, in order to elucidate structural and spectral properties of the investigated molecule. Experimental vibrational spectra are found to be in accord with the simulated vibrational spectra. The assignment of the vibrational modes was performed depending on the calculated potential energy distribution (PED). In slico molecular docking of cyclo(Ala-His) was also carried out with DNA. The drug likeness and ADMET properties were analyzed for the prediction of pharmacokinetic profiles. The results revealed that the compound has the potential to be the leading molecule in the drug discovery process.
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Affiliation(s)
- Sefa Celik
- Physics Department, Science Faculty, Istanbul University, Istanbul, Turkey
| | - Gozde Yilmaz
- Alternative Energy Resources Program, Vocational School, Istanbul Kultur University, Istanbul, Turkey
| | - Aysen E Ozel
- Physics Department, Science Faculty, Istanbul University, Istanbul, Turkey
| | - Sevim Akyuz
- Physics Department, Science and Letters Faculty, Istanbul Kultur University, Istanbul, Turkey
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Celik S, Albayrak AT, Akyuz S, Ozel AE, Sigirci BD. Synthesis, antimicrobial activity, molecular docking and ADMET study of a caprolactam-glycine cluster. J Biomol Struct Dyn 2020; 39:2376-2386. [PMID: 32216608 DOI: 10.1080/07391102.2020.1748112] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Density functional theory calculations were performed with DFT method using both b3lyp/6-311++G(d,p) and wb97xd/6-311++G(d,p) levels of theory to predict the molecular geometry, to evaluate the molecular electrostatic potential and frontier molecular orbitals of synthesized a new compound: caprolactam-glysine cluster (CL-Gly). Molecular docking study of the CL-Gly was carried out to clarify the interaction and the probable binding modes, between the title compound and DNA. The antibacterial activities of CL-Gly cluster against Gram-positive and Gram-negative bacteria was determined. In silico ADMET study was also performed for predicting pharmacokinetic and toxicity profile of the synthesized cluster which expressed good drug-like behavior and non-toxic nature. It was revealed that the compound has importance in drug discovery process.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sefa Celik
- Physics Department, Science Faculty, Istanbul University, Vezneciler, Istanbul, Turkey
| | - Ali Tugrul Albayrak
- Chemical Engineering Department, Engineering Faculty, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Sevim Akyuz
- Physics Department, Science and Letters Faculty, Istanbul Kultur University, Istanbul, Turkey
| | - Aysen E Ozel
- Physics Department, Science Faculty, Istanbul University, Vezneciler, Istanbul, Turkey
| | - Belgi Diren Sigirci
- Department of Microbiology, Faculty of Veterinary Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
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The effect of ellagic acid on caspase-3/bcl-2/Nrf-2/NF-kB/TNF-α /COX-2 gene expression product apoptosis pathway: a new approach for muscle damage therapy. Mol Biol Rep 2020; 47:2573-2582. [DOI: 10.1007/s11033-020-05340-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 01/14/2020] [Indexed: 02/06/2023]
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