{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T02:39:39Z","timestamp":1787020779755,"version":"build-2736575974"},"reference-count":44,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,7,30]],"date-time":"2024-07-30T00:00:00Z","timestamp":1722297600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2024,7,30]],"date-time":"2024-07-30T00:00:00Z","timestamp":1722297600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/501100004054","name":"King Abdulaziz University","doi-asserted-by":"crossref","award":["IFPIP: 636-140-1443"],"award-info":[{"award-number":["IFPIP: 636-140-1443"]}],"id":[{"id":"10.13039\/501100004054","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Chemistry"],"DOI":"10.1186\/s13065-024-01251-x","type":"journal-article","created":{"date-parts":[[2024,7,30]],"date-time":"2024-07-30T14:03:05Z","timestamp":1722348185000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["Marine fungal diversity unlocks potent antivirals against monkeypox through methyltransferase inhibition revealed by molecular dynamics and free energy landscape"],"prefix":"10.1186","volume":"18","author":[{"given":"Azzah S.","family":"Alharbi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah A.","family":"Altwaim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mai M.","family":"El-Daly","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ahmed M.","family":"Hassan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ibrahim A.","family":"AL-Zahrani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leena H.","family":"Bajrai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isra M.","family":"Alsaady","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vivek Dhar","family":"Dwivedi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Esam I.","family":"Azhar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,7,30]]},"reference":[{"key":"1251_CR1","unstructured":"WHO. Mpox (monkeypox). 2023. https:\/\/www.who.int\/news-room\/fact-sheets\/detail\/monkeypox. Accessed 25 Nov 2023."},{"key":"1251_CR2","doi-asserted-by":"publisher","first-page":"2259","DOI":"10.1038\/s41467-023-38019-1","volume":"14","author":"J Silhan","year":"2023","unstructured":"Silhan J, Klima M, Otava T, Skvara P, Chalupska D, Chalupsky K, et al. Discovery and structural characterization of monkeypox virus methyltransferase VP39 inhibitors reveal similarities to SARS-CoV-2 nsp14 methyltransferase. Nat Commun. 2023;14:2259.","journal-title":"Nat Commun"},{"key":"1251_CR3","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1016\/j.virol.2015.01.019","volume":"479\u2013480","author":"JL Hyde","year":"2015","unstructured":"Hyde JL, Diamond MS. Innate immune restriction and antagonism of viral RNA lacking 2\u05f3-O methylation. Virology. 2015;479\u2013480:66\u201374.","journal-title":"Virology"},{"key":"1251_CR4","doi-asserted-by":"publisher","first-page":"320","DOI":"10.1016\/j.chom.2015.02.002","volume":"17","author":"S-W Liu","year":"2015","unstructured":"Liu S-W, Katsafanas GC, Liu R, Wyatt LS, Moss B. Poxvirus decapping enzymes enhance virulence by preventing the accumulation of dsRNA and the induction of innate antiviral responses. Cell Host Microbe. 2015;17:320\u201331.","journal-title":"Cell Host Microbe"},{"key":"1251_CR5","doi-asserted-by":"publisher","first-page":"957","DOI":"10.1007\/s40265-022-01742-y","volume":"82","author":"JG Rizk","year":"2022","unstructured":"Rizk JG, Lippi G, Henry BM, Forthal DN, Rizk Y. Prevention and Treatment of Monkeypox. Drugs. 2022;82:957\u201363.","journal-title":"Drugs"},{"key":"1251_CR6","doi-asserted-by":"publisher","DOI":"10.1016\/j.tibs.2022.04.010","author":"C Grimm","year":"2022","unstructured":"Grimm C, Bartuli J, Fischer U. Cytoplasmic gene expression: lessons from poxviruses. Trends Biochem Sci. 2022. https:\/\/doi.org\/10.1016\/j.tibs.2022.04.010.","journal-title":"Trends Biochem Sci."},{"key":"1251_CR7","first-page":"88","volume":"2","author":"X Shi","year":"1996","unstructured":"Shi X, Yao P, Jose T, Gershon P. Methyltransferase-specific domains within VP-39, a bifunctional protein that participates in the modification of both mRNA ends. RNA. 1996;2:88\u2013101.","journal-title":"RNA"},{"key":"1251_CR8","unstructured":"WHO. Disease Outbreak News; Multi-country monkeypox outbreak in non-endemic countries. 2022. Available at: https:\/\/www.who.int\/emergencies\/disease-outbreak-news\/item\/2022-DON385. Accessed 25 Nov 2023."},{"key":"1251_CR9","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1016\/j.phytol.2017.11.003","volume":"23","author":"S Agrawal","year":"2018","unstructured":"Agrawal S, Adholeya A, Barrow CJ, Deshmukh SK. Marine fungi: an untapped bioresource for future cosmeceuticals. Phytochem Lett. 2018;23:15\u201320.","journal-title":"Phytochem Lett"},{"key":"1251_CR10","doi-asserted-by":"publisher","DOI":"10.1016\/j.phrs.2022.106391","volume":"183","author":"AMS Mayer","year":"2022","unstructured":"Mayer AMS, Pierce ML, Howe K, Rodr\u00edguez AD, Taglialatela-Scafati O, Nakamura F, et al. Marine pharmacology in 2018: marine compounds with antibacterial, antidiabetic, antifungal, anti-inflammatory, antiprotozoal, antituberculosis and antiviral activities; affecting the immune and nervous systems, and other miscellaneous mechanisms of action. Pharmacol Res. 2022;183: 106391.","journal-title":"Pharmacol Res"},{"key":"1251_CR11","doi-asserted-by":"publisher","first-page":"11104","DOI":"10.1002\/jcb.28387","volume":"120","author":"G Tanwar","year":"2019","unstructured":"Tanwar G, Purohit R. Gain of native conformation of Aurora A S155R mutant by small molecules. J of Cellular Biochemistry. 2019;120:11104\u201314.","journal-title":"J of Cellular Biochemistry"},{"key":"1251_CR12","doi-asserted-by":"publisher","DOI":"10.1080\/07391102.2021.1900918","author":"R Singh","year":"2022","unstructured":"Singh R, Bhardwaj VK, Sharma J, Das P, Purohit R. Identification of selective cyclin-dependent kinase 2 inhibitor from the library of pyrrolone-fused benzosuberene compounds: an in silico exploration. J Biomol Struct Dynam. 2022. https:\/\/doi.org\/10.1080\/07391102.2021.1900918.","journal-title":"J Biomol Struct Dynam"},{"key":"1251_CR13","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1093\/nar\/28.1.235","volume":"28","author":"HM Berman","year":"2000","unstructured":"Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, et al. The protein data bank. Nucleic Acids Res. 2000;28:235\u201342.","journal-title":"Nucleic Acids Res"},{"key":"1251_CR14","doi-asserted-by":"publisher","first-page":"D509","DOI":"10.1093\/nar\/gkaa763","volume":"49","author":"C Lyu","year":"2021","unstructured":"Lyu C, Chen T, Qiang B, Liu N, Wang H, Zhang L, et al. CMNPD: a comprehensive marine natural products database towards facilitating drug discovery from the ocean. Nucleic Acids Res. 2021;49:D509\u201315.","journal-title":"Nucleic Acids Res"},{"key":"1251_CR15","doi-asserted-by":"publisher","first-page":"1605","DOI":"10.1002\/jcc.20084","volume":"25","author":"EF Pettersen","year":"2004","unstructured":"Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, et al. UCSF Chimera\u2013a visualization system for exploratory research and analysis. J Comput Chem. 2004;25:1605\u201312.","journal-title":"J Comput Chem"},{"key":"1251_CR16","doi-asserted-by":"publisher","first-page":"W448","DOI":"10.1093\/nar\/gkv306","volume":"43","author":"CM Labb\u00e9","year":"2015","unstructured":"Labb\u00e9 CM, Rey J, Lagorce D, Vavru\u0161a M, Becot J, Sperandio O, et al. MTiOpenScreen: a web server for structure-based virtual screening. Nucleic Acids Res. 2015;43:W448\u201354.","journal-title":"Nucleic Acids Res"},{"key":"1251_CR17","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1016\/j.ddtec.2004.11.007","volume":"1","author":"CA Lipinski","year":"2004","unstructured":"Lipinski CA. Lead- and drug-like compounds: the rule-of-five revolution. Drug Discov Today Technol. 2004;1:337\u201341.","journal-title":"Drug Discov Today Technol"},{"key":"1251_CR18","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1002\/jcc.21334","volume":"31","author":"O Trott","year":"2010","unstructured":"Trott O, Olson AJ. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading. J Comput Chem. 2010;31:455\u201361.","journal-title":"J Comput Chem"},{"key":"1251_CR19","doi-asserted-by":"publisher","DOI":"10.1080\/07391102.2023.2292794","author":"PC Mishra","year":"2023","unstructured":"Mishra PC, Alanazi AM, Panda SP, Alam A, Dubey A, Jha SK, et al. Computational exploration of Zika virus RNA-dependent RNA polymerase inhibitors: a promising antiviral drug discovery approach. J Biomol Struct Dynam. 2023. https:\/\/doi.org\/10.1080\/07391102.2023.2292794.","journal-title":"J Biomol Struct Dynam"},{"key":"1251_CR20","doi-asserted-by":"publisher","first-page":"34","DOI":"10.3390\/md22010034","volume":"22","author":"AS Alawam","year":"2024","unstructured":"Alawam AS, Alawam HS, Alshahrani MM, Alwethaynani MS, Alneghery LM, Alamri MA. Structural and dynamical basis of VP35-RBD inhibition by marine fungi compounds to combat marburg virus infection. Marine Drugs. 2024;22:34.","journal-title":"Marine Drugs."},{"key":"1251_CR21","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0077453","volume":"8","author":"A Kumar","year":"2013","unstructured":"Kumar A, Rajendran V, Sethumadhavan R, Purohit R. Molecular dynamic simulation reveals damaging impact of RAC1 F28L mutation in the switch I region. PLoS ONE. 2013;8: e77453.","journal-title":"PLoS ONE"},{"key":"1251_CR22","doi-asserted-by":"publisher","first-page":"671","DOI":"10.1002\/jcc.21367","volume":"31","author":"K Vanommeslaeghe","year":"2010","unstructured":"Vanommeslaeghe K, Hatcher E, Acharya C, Kundu S, Zhong S, Shim J, et al. CHARMM General Force Field (CGenFF): A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J Comput Chem. 2010;31:671.","journal-title":"J Comput Chem"},{"key":"1251_CR23","doi-asserted-by":"publisher","first-page":"911","DOI":"10.1080\/07391102.2020.1720818","volume":"39","author":"J Sharma","year":"2021","unstructured":"Sharma J, Bhardwaj VK, Das P, Purohit R. Identification of naturally originated molecules as \u03b3-aminobutyric acid receptor antagonist. J Biomol Struct Dyn. 2021;39:911\u201322.","journal-title":"J Biomol Struct Dyn"},{"key":"1251_CR24","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","volume":"1","author":"MJ Abraham","year":"2015","unstructured":"Abraham MJ, Murtola T, Schulz R, P\u00e1ll S, Smith JC, Hess B, et al. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX. 2015;1:19\u201325.","journal-title":"SoftwareX"},{"key":"1251_CR25","doi-asserted-by":"publisher","first-page":"1701","DOI":"10.1002\/jcc.20291","volume":"26","author":"D Van Der Spoel","year":"2005","unstructured":"Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ. GROMACS: fast, flexible, and free. J Comput Chem. 2005;26:1701\u201318.","journal-title":"J Comput Chem"},{"key":"1251_CR26","doi-asserted-by":"publisher","first-page":"9954","DOI":"10.1021\/jp003020w","volume":"105","author":"P Mark","year":"2001","unstructured":"Mark P, Nilsson L. Structure and dynamics of the TIP3P, SPC, and SPC\/E water models at 298 K. J Phys Chem A. 2001;105:9954\u201360.","journal-title":"J Phys Chem A"},{"key":"1251_CR27","first-page":"3525","volume":"5","author":"B Jaidhan","year":"2014","unstructured":"Jaidhan B, Rao PS, Apparao A. Energy minimization and conformation analysis of molecules using steepest descent method. Int J Comput Sci Inf Technol. 2014;5:3525\u20138.","journal-title":"Int J Comput Sci Inf Technol"},{"key":"1251_CR28","doi-asserted-by":"publisher","first-page":"124108","DOI":"10.1063\/1.4978807","volume":"146","author":"Y Lin","year":"2017","unstructured":"Lin Y, Pan D, Li J, Zhang L, Shao X. Application of Berendsen barostat in dissipative particle dynamics for nonequilibrium dynamic simulation. J Chem Phys. 2017;146:124108.","journal-title":"J Chem Phys."},{"key":"1251_CR29","unstructured":"Essential dynamics sampling\u2014GROMACS 2023. 3 Documentation. https:\/\/manual.gromacs.org\/current\/reference-manual\/algorithms\/essential-dynamics.html. Accessed 19 Jan 2024."},{"key":"1251_CR30","volume-title":"Matplotlib for Python developers","author":"S Tosi","year":"2009","unstructured":"Tosi S. Matplotlib for Python developers. Birmingham: Packt Publishing Ltd; 2009."},{"key":"1251_CR31","volume-title":"Matplotlib for Python developers: effective techniques for data visualization with Python","author":"A Yim","year":"2018","unstructured":"Yim A, Chung C, Yu A. Matplotlib for Python developers: effective techniques for data visualization with Python. Birmingham: Packt Publishing Ltd; 2018."},{"key":"1251_CR32","doi-asserted-by":"publisher","first-page":"1605","DOI":"10.1002\/jcc.20084","volume":"25","author":"EF Pettersen","year":"2004","unstructured":"Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, et al. UCSF Chimera\u2014a visualization system for exploratory research and analysis. J Comput Chem. 2004;25:1605\u201312.","journal-title":"J Comput Chem"},{"key":"1251_CR33","first-page":"682","volume-title":"Maestro","author":"S Maestro","year":"2020","unstructured":"Maestro S. Maestro. New York: Schr\u00f6dinger, LLC; 2020. p. 682."},{"key":"1251_CR34","doi-asserted-by":"publisher","DOI":"10.1007\/s12013-013-9572-1","author":"A Kumar","year":"2013","unstructured":"Kumar A, Rajendran V, Sethumadhavan R, Purohit R. Evidence of colorectal cancer-associated mutation in MCAK: a computational report. Cell Biochem Biophys. 2013. https:\/\/doi.org\/10.1007\/s12013-013-9572-1.","journal-title":"Cell Biochem Biophys"},{"key":"1251_CR35","unstructured":"A K, V R, R S, P S, S T, R P. Computational SNP analysis: current approaches and future prospects. PubMed."},{"key":"1251_CR36","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1021\/ct9005745","volume":"6","author":"GG Maisuradze","year":"2010","unstructured":"Maisuradze GG, Liwo A, Scheraga HA. Relation between free energy landscapes of proteins and dynamics. J Chem Theory Comput. 2010;6:583\u201395.","journal-title":"J Chem Theory Comput"},{"key":"1251_CR37","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1007\/s12551-011-0063-6","volume":"4","author":"J Higo","year":"2012","unstructured":"Higo J, Ikebe J, Kamiya N, Nakamura H. Enhanced and effective conformational sampling of protein molecular systems for their free energy landscapes. Biophys Rev. 2012;4:27\u201344.","journal-title":"Biophys Rev"},{"key":"1251_CR38","doi-asserted-by":"publisher","first-page":"889","DOI":"10.1016\/j.jmgm.2009.01.006","volume":"27","author":"E Papaleo","year":"2009","unstructured":"Papaleo E, Mereghetti P, Fantucci P, Grandori R, De Gioia L. Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: the myoglobin case. J Mol Graph Model. 2009;27:889\u201399.","journal-title":"J Mol Graph Model"},{"key":"1251_CR39","doi-asserted-by":"publisher","first-page":"13497","DOI":"10.1080\/07391102.2021.1989040","volume":"40","author":"M Kumari","year":"2022","unstructured":"Kumari M, Singh R, Subbarao N. Exploring the interaction mechanism between potential inhibitor and multi-target Mur enzymes of mycobacterium tuberculosis using molecular docking, molecular dynamics simulation, principal component analysis, free energy landscape, dynamic cross-correlation matrices, vector movements, and binding free energy calculation. J Biomol Struct Dyn. 2022;40:13497\u2013526.","journal-title":"J Biomol Struct Dyn"},{"key":"1251_CR40","doi-asserted-by":"publisher","first-page":"W5","DOI":"10.1093\/nar\/gkab255","volume":"49","author":"G Xiong","year":"2021","unstructured":"Xiong G, Wu Z, Yi J, Fu L, Yang Z, Hsieh C, et al. ADMETlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties. Nucleic Acids Res. 2021;49:W5-14.","journal-title":"Nucleic Acids Res."},{"key":"1251_CR41","doi-asserted-by":"publisher","first-page":"5241","DOI":"10.3390\/molecules27165241","volume":"27","author":"S Faisal","year":"2022","unstructured":"Faisal S, Badshah SL, Kubra B, Sharaf M, Emwas A-H, Jaremko M, et al. Identification and inhibition of the druggable allosteric site of SARS-CoV-2 NSP10\/NSP16 methyltransferase through computational approaches. Molecules. 2022;27:5241.","journal-title":"Molecules"},{"key":"1251_CR42","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1007\/978-1-62703-658-0_11","volume":"1084","author":"CC David","year":"2014","unstructured":"David CC, Jacobs DJ. Principal component analysis: a method for determining the essential dynamics of proteins. Methods Mol Biol. 2014;1084:193\u2013226.","journal-title":"Methods Mol Biol"},{"key":"1251_CR43","doi-asserted-by":"publisher","first-page":"852","DOI":"10.1002\/jcb.30232","volume":"123","author":"R Alexey","year":"2022","unstructured":"Alexey R, Dariya S, Liudmyla I, Lilia V, Valeriy M, Dmytro L, et al. Structure-based virtual screening and biological evaluation of novel inhibitors of mycobacterium Z-ring formation. J Cell Biochem. 2022;123:852\u201362.","journal-title":"J Cell Biochem"},{"key":"1251_CR44","doi-asserted-by":"publisher","DOI":"10.3390\/molecules26020475","author":"R Baptista","year":"2021","unstructured":"Baptista R, Bhowmick S, Shen J, Mur LAJ. Molecular docking suggests the targets of anti-mycobacterial natural products. Molecules. 2021. https:\/\/doi.org\/10.3390\/molecules26020475.","journal-title":"Molecules"}],"container-title":["BMC Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13065-024-01251-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s13065-024-01251-x\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13065-024-01251-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,30]],"date-time":"2024-07-30T14:12:35Z","timestamp":1722348755000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcchem.biomedcentral.com\/articles\/10.1186\/s13065-024-01251-x"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,7,30]]},"references-count":44,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["1251"],"URL":"https:\/\/doi.org\/10.1186\/s13065-024-01251-x","relation":{},"ISSN":["2661-801X"],"issn-type":[{"value":"2661-801X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,7,30]]},"assertion":[{"value":"10 May 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 July 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"30 July 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"141"}}