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Akash S, Mir SA, Mahmood S, Hossain S, Islam MR, Mukerjee N, Nayak B, Nafidi HA, Bin Jardan YA, Mekonnen A, Bourhia M. Novel computational and drug design strategies for inhibition of monkeypox virus and Babesia microti: molecular docking, molecular dynamic simulation and drug design approach by natural compounds. Front Microbiol 2023; 14:1206816. [PMID: 37538847 PMCID: PMC10394520 DOI: 10.3389/fmicb.2023.1206816] [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: 04/16/2023] [Accepted: 06/20/2023] [Indexed: 08/05/2023] Open
Abstract
Background The alarming increase in tick-borne pathogens such as human Babesia microti is an existential threat to global public health. It is a protozoan parasitic infection transmitted by numerous species of the genus Babesia. Second, monkeypox has recently emerged as a public health crisis, and the virus has spread around the world in the post-COVID-19 period with a very rapid transmission rate. These two novel pathogens are a new concern for human health globally and have become a significant obstacle to the development of modern medicine and the economy of the whole world. Currently, there are no approved drugs for the treatment of this disease. So, this research gap encourages us to find a potential inhibitor from a natural source. Methods and materials In this study, a series of natural plant-based biomolecules were subjected to in-depth computational investigation to find the most potent inhibitors targeting major pathogenic proteins responsible for the diseases caused by these two pathogens. Results Among them, most of the selected natural compounds are predicted to bind tightly to the targeted proteins that are crucial for the replication of these novel pathogens. Moreover, all the molecules have outstanding ADMET properties such as high aqueous solubility, a higher human gastrointestinal absorption rate, and a lack of any carcinogenic or hepatotoxic effects; most of them followed Lipinski's rule. Finally, the stability of the compounds was determined by molecular dynamics simulations (MDs) for 100 ns. During MDs, we observed that the mentioned compounds have exceptional stability against selected pathogens. Conclusion These advanced computational strategies reported that 11 lead compounds, including dieckol and amentoflavone, exhibited high potency, excellent drug-like properties, and no toxicity. These compounds demonstrated strong binding affinities to the target enzymes, especially dieckol, which displayed superior stability during molecular dynamics simulations. The MM/PBSA method confirmed the favorable binding energies of amentoflavone and dieckol. However, further in vitro and in vivo studies are necessary to validate their efficacy. Our research highlights the role of Dieckol and Amentoflavone as promising candidates for inhibiting both monkeypox and Babesia microti, demonstrating their multifaceted roles in the control of these pathogens.
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Affiliation(s)
- Shopnil Akash
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International, University, Dhaka, Bangladesh
| | - Showkat Ahmad Mir
- School of Life Sciences, Sambalpur University, Sambalpur, Odisha, India
| | - Sajjat Mahmood
- Department of Microbiology, Jagannath University, Dhaka, Bangladesh
| | - Saddam Hossain
- Department of Biomedical Engineering, Faculty of Engineering and Technology, Islamic University, Kushtia, Bangladesh
| | - Md. Rezaul Islam
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International, University, Dhaka, Bangladesh
| | - Nobendu Mukerjee
- Department of Microbiology, West Bengal State University, Kolkata, West Bengal, India
| | - Binata Nayak
- School of Life Sciences, Sambalpur University, Sambalpur, Odisha, India
| | - Hiba-Allah Nafidi
- Department of Food Science, Faculty of Agricultural and Food Sciences, Laval University, Quebec City, QC, Canada
| | - Yousef A. Bin Jardan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Amare Mekonnen
- Department of Biology, Bahir Dar University, Bahir Dar, Ethiopia
| | - Mohammed Bourhia
- Department of Chemistry and Biochemistry, Faculty of Medicine and Pharmacy, Ibn Zohr University, Laayoune, Morocco
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Investigation of spectroscopic properties and molecular dynamics simulations of the interaction of mebendazole with β-cyclodextrin. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2021. [DOI: 10.1007/s13738-020-02006-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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In Silico Study Reveals How E64 Approaches, Binds to, and Inhibits Falcipain-2 of Plasmodium falciparum that Causes Malaria in Humans. Sci Rep 2018; 8:16380. [PMID: 30401806 PMCID: PMC6219542 DOI: 10.1038/s41598-018-34622-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 10/23/2018] [Indexed: 11/08/2022] Open
Abstract
Plasmodium falciparum malaria, which degrades haemoglobin through falcipain-2 (FP2), is a serious disease killing 445 thousand people annually. Since the P. falciparum's survival in humans depends on its ability to degrade human's haemoglobin, stoppage or hindrance of FP2 has antimalarial effects. Therefore, we studied the atomic details of how E64 approaches, binds to, and inhibits FP2. We found that E64 (1) gradually approaches FP2 by first interacting with FP2's D170 and Q171 or N81, N77, and K76; (2) binds FP2 tightly (ΔGbinding = -12.2 ± 1.1 kJ/mol); and (3) persistently blocks access to FP2's catalytic residues regardless of whether or not E64 has already been able to form a covalent bond with FP2's C42. Furthermore, the results suggest that S41, D234, D170, N38, N173, and L172 (which are located in or near the FP2's catalytic site's binding pocket) contribute the most towards the favourable binding of E64 to FP2. Their in silico mutations adversely affect E64-FP2 binding affinity with D234L/A, N173L/A, W43F/A, D234L/A, H174F/A, and N38L/A having the most significant adverse effects on E64-FP2 binding and interactions. The findings presented in this article, which has antimalarial implications, suggest that hydrogen bonding and electrostatic interactions play important roles in E64-FP2 binding, and that a potential FP2-blocking E64-based/E64-like antimalarial drug should be capable of being both hydrogen-bond donor and acceptor, and/or have the ability to favourably interact with polar amino acids (such as S41, S149, N38, N173, N77, Q171) and with charged amino acids (such as D234, D170, H174) of FP2. The abilities to favourably interact with ASN, ASP, and SER appears to be important characteristics that such potential drug should have.
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Mary V, Haris P, Varghese MK, Aparna P, Sudarsanakumar C. Experimental Probing and Molecular Dynamics Simulation of the Molecular Recognition of DNA Duplexes by the Flavonoid Luteolin. J Chem Inf Model 2017; 57:2237-2249. [PMID: 28825481 DOI: 10.1021/acs.jcim.6b00747] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Luteolin (C15H10O6) is an important flavonoid found in many fruits, plants, medicinal herbs, and vegetables exhibiting many pharmacological properties. The anticancer, antitumor, antioxidant, and anti-inflammatory activities of luteolin have been reported. The pharmacological action of small molecules is dependent upon its interaction with biomacromolecules. The interactions of small molecules with DNA play a major role in the transcription and translation process. In this work, we explored the energetic profile of DNA-luteolin interaction by isothermal titration calorimetry (ITC). The effect of temperature and salt concentration on DNA binding was examined by UV-Vis method. The mode of interaction was further probed by UV melting temperature analysis and differential scanning calorimetry. An atomic level insight on the recognition of luteolin with DNA was achieved by employing molecular dynamics (MD) simulation on luteolin in complex with AT- and GC-rich DNA sequences. AMBER force field proves to be appropriate in providing an understanding on the binding mode and specificity of luteolin with duplex DNA. MD results suggest a minor groove binding of luteolin with DNA and the binding free energy obtained is in agreement with the experimental results.
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Affiliation(s)
- Varughese Mary
- School of Pure and Applied Physics, Mahatma Gandhi University , Kottayam, Kerala 686560, India
| | - P Haris
- School of Pure and Applied Physics, Mahatma Gandhi University , Kottayam, Kerala 686560, India
| | - Mathew K Varghese
- School of Pure and Applied Physics, Mahatma Gandhi University , Kottayam, Kerala 686560, India.,Department of Physics, Pavanatma College , Murickassery, Kerala 685604, India
| | - P Aparna
- School of Pure and Applied Physics, Mahatma Gandhi University , Kottayam, Kerala 686560, India
| | - C Sudarsanakumar
- School of Pure and Applied Physics, Mahatma Gandhi University , Kottayam, Kerala 686560, India.,Center for High Performance Computing, Mahatma Gandhi University , Kottayam, Kerala 686560, India
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Cova TFGG, Nunes SCC, Pais AACC. Free-energy patterns in inclusion complexes: the relevance of non-included moieties in the stability constants. Phys Chem Chem Phys 2017; 19:5209-5221. [DOI: 10.1039/c6cp08081b] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A MD/PMF-based procedure is designed for quantification of the interaction and respective components, guiding complex formation in water between β-CD and several naphthalene derivatives, highlighting the relevance of substituents.
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Affiliation(s)
- Tânia F. G. G. Cova
- Coimbra Chemistry Centre
- Department of Chemistry
- University of Coimbra
- 3004-535 Coimbra
- Portugal
| | - Sandra C. C. Nunes
- Coimbra Chemistry Centre
- Department of Chemistry
- University of Coimbra
- 3004-535 Coimbra
- Portugal
| | - Alberto A. C. C. Pais
- Coimbra Chemistry Centre
- Department of Chemistry
- University of Coimbra
- 3004-535 Coimbra
- Portugal
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Haris P, Mary V, Haridas M, Sudarsanakumar C. Energetics, Thermodynamics, and Molecular Recognition of Piperine with DNA. J Chem Inf Model 2015; 55:2644-56. [DOI: 10.1021/acs.jcim.5b00514] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
| | | | - M. Haridas
- Inter
University Centre for Bioscience, Kannur University, Thalassery
Campus, Palayad, Kerala 670661, India
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Kocakaya SÖ, Turgut Y, Pirinççioglu N. Enantiomeric discrimination of chiral organic salts by chiral aza-15-crown-5 ether with C 1 symmetry: experimental and theoretical approaches. J Mol Model 2015; 21:55. [PMID: 25701087 DOI: 10.1007/s00894-015-2604-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 02/01/2015] [Indexed: 11/25/2022]
Abstract
The work involves an experimental ((1)H NMR) and theoretical (MD, MM-PBSA and DFT) investigation of the molecular recognition and discrimination properties of a chiral aza-15-crown-5 against methyl esters of alanine, phenylalanine and valine hydrochloride salts. The results indicate that the receptor binds enantiomers with moderate binding constants (88-1,389 M(-1)), with phenylalanine being more discriminated. The difference in experimental binding free energies (ΔG(R) - ΔG(S)) for alanine, phenylalanine and valine enantiomers were calculated as -0.36, -1.58 and 0.80 kcal mol(-1), respectively. The differences in theoretical binding energies were calculated by MM-PBSA (ΔE(R)PB - ΔE(S)PB=) as -0.30, -1.45 and 0.88, by B3LYP/6-31+G(d) as -1.17, -0.84 and 0.74 and by M06-2X/6-31+G(d) as -1.40, -3.26 and 1.66 kcal mol(-1). The data obtained give valuable information regarding the molecular recognition mode of the organoammonium complexes of chiral aza-crown ether with C 1 symmetry, which may be relevant to biological systems.
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Affiliation(s)
- Safak Özhan Kocakaya
- Department of Chemistry, Faculty of Science, University of Dicle, Diyarbakir, 21280, Turkey
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Wallace SJ, Kee TW, Huang DM. Molecular Basis of Binding and Stability of Curcumin in Diamide-Linked γ-Cyclodextrin Dimers. J Phys Chem B 2013; 117:12375-82. [DOI: 10.1021/jp406125x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Samuel J. Wallace
- School of Chemistry and Physics, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Tak W. Kee
- School of Chemistry and Physics, The University of Adelaide, Adelaide, SA 5005, Australia
| | - David M. Huang
- School of Chemistry and Physics, The University of Adelaide, Adelaide, SA 5005, Australia
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Zhang H, Tan T, Hetényi C, van der Spoel D. Quantification of Solvent Contribution to the Stability of Noncovalent Complexes. J Chem Theory Comput 2013; 9:4542-51. [DOI: 10.1021/ct400404q] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Haiyang Zhang
- Beijing Key Laboratory
of Bioprocess, Department of Biochemical Engineering, Beijing University of Chemical Technology, Box 53, 100029 Beijing, China
- Science for Life
Laboratory, Department of Cell and Molecular Biology, Uppsala University, Husargatan
3, Box 596, SE-751 24 Uppsala, Sweden
| | - Tianwei Tan
- Beijing Key Laboratory
of Bioprocess, Department of Biochemical Engineering, Beijing University of Chemical Technology, Box 53, 100029 Beijing, China
| | - Csaba Hetényi
- Molecular Biophysics
Research Group, Hungarian Academy of Sciences, Pázmány sétány 1/C, H-1117 Budapest, Hungary
| | - David van der Spoel
- Science for Life
Laboratory, Department of Cell and Molecular Biology, Uppsala University, Husargatan
3, Box 596, SE-751 24 Uppsala, Sweden
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