اكتشاف مثبط إستروزي لأنزيم برويل-تي آر إن إيه المحتمل عبر الفحص الافتراضي والتجربة في المختبر ضد البلاسموديوم فالسيباروم

Smith RD, Keogh-Brown MR, Chico RM, Bretscher MT, Drakeley C, Jensen HT. Will More of the Same Achieve Malaria Elimination? Results from an Integrated Macroeconomic Epidemiological Demographic Model. Am J Trop Med Hyg. 2020 Nov; 103 (5):1871–82. DOI: https://doi.org/10.4269/ajtmh.19-0472

WHO. Word Malaria Report 2021. Word Malaria report Geneva: World Health Organization. (2021). Licence: CC. 2021. 2013–2015 p.

Mishra KP, Ganju L, Sairam M, Banerjee PK, Sawhney RC. A review of high throughput technology for the screening of natural products. Biomed Pharmacother [Internet]. 2008 cited 2008; 62 (2):94–8. Available from: https://www.sciencedirect.com/science/article/pii/S0753332207001278 DOI: https://doi.org/10.1016/j.biopha.2007.06.012

Tanrikulu Y, Krüger B, Proschak E. The holistic integration of virtual screening in drug discovery. Drug Discov Today. 2013 Apr; 18 (7–8):358–64. DOI: https://doi.org/10.1016/j.drudis.2013.01.007

Nyamai DW, Tastan Bishop Ö. Identification of Selective Novel Hits against Plasmodium falciparum Prolyl tRNA Synthetase Active Site and a Predicted Allosteric Site Using in silico Approaches. Int J Mol Sci. 2020 May; 21 (11).

Shah P, Tiwari S, Siddiqi MI. Recent progress in the identification and development of anti-malarial agents using virtual screening based approaches. Comb Chem High Throughput Screen. 2015; 18 (3):257–68. DOI: https://doi.org/10.2174/1386207318666150305154913

Ripphausen P, Nisius B, Bajorath J. State-of-the-art in ligand-based virtual screening. Drug Discov Today. 2011 May; 16 (9–10):372–6. DOI: https://doi.org/10.1016/j.drudis.2011.02.011

Varela-Rial A, Majewski M, De Fabritiis G. Structure based virtual screening: Fast and slow. WIREs Comput Mol Sci [Internet]. 2022 Mar 1 cited 2022; 12 (2):e1544. Available from: https://doi.org/10.1002/wcms.1544 DOI: https://doi.org/10.1002/wcms.1544

Widyananda MH, Kurniasari CA, Alam FM, Rizky WC, Dings TGA, Ansori ANM, et al. Exploration of Potentially Bioactive Compounds from Fingerroot (Boesenbergia rotunda L.) as Inhibitor of Atherosclerosis-Related Proteins (CETP, ACAT1, OSC, sPLA2): An in silico Study. Jordan J Pharm Sci. 2023; 16 (3):550–64. DOI: https://doi.org/10.35516/jjps.v16i3.1609

Babandi A, Anosike CA, Ezeanyika LUS, Yelekçi K, Uba AI. Molecular modeling studies of some phytoligands from Ficus sycomorus fraction as potential inhibitors of cytochrome CYP6P3 enzyme of Anopheles coluzzii. Jordan J Pharm Sci. 2022; 15 (2):258–75. DOI: https://doi.org/10.35516/jjps.v15i2.324

Ghislat G, Rahman T, Ballester PJ. Recent progress on the prospective application of machine learning to structure-based virtual screening. Curr Opin Chem Biol. 2021 Dec; 65:28–34. DOI: https://doi.org/10.1016/j.cbpa.2021.04.009

Kimber TB, Chen Y, Volkamer A. Deep Learning in Virtual Screening: Recent Applications and Developments. Int J Mol Sci. 2021 Apr; 22 (9). DOI: https://doi.org/10.3390/ijms22094435

Ibba M, Soll D. Aminoacyl-tRNA synthesis. Annu Rev Biochem. 2000; 69:617–50. DOI: https://doi.org/10.1146/annurev.biochem.69.1.617

Manickam Y, Chaturvedi R, Babbar P, Malhotra N, Jain V, Sharma A. Drug targeting of one or more aminoacyl-tRNA synthetase in the malaria parasite Plasmodium falciparum. Drug Discov Today. 2018 Jun; 23 (6):1233–40. DOI: https://doi.org/10.1016/j.drudis.2018.01.050

Keller TL, Zocco D, Sundrud MS, Hendrick M, Edenius M, Yum J, et al. Halofuginone and other febrifugine derivatives inhibit prolyl-tRNA synthetase. Nat Chem Biol. 2012 Feb; 8 (3):311–7. DOI: https://doi.org/10.1038/nchembio.790

Herman JD, Pepper LR, Cortese JF, Estiu G, Galinsky K, Zuzarte-Luis V, et al. The cytoplasmic prolyl-tRNA synthetase of the malaria parasite is a dual-stage target of febrifugine and its analogs. Sci Transl Med. 2015 May; 7 (288):288ra77. DOI: https://doi.org/10.1126/scitranslmed.aaa3575

Jain V, Yogavel M, Kikuchi H, Oshima Y, Hariguchi N, Matsumoto M, et al. Targeting Prolyl-tRNA Synthetase to Accelerate Drug Discovery against Malaria, Leishmaniasis, Toxoplasmosis, Cryptosporidiosis, and Coccidiosis. Structure. 2017 Oct; 25 (10):1495-1505.e6. DOI: https://doi.org/10.1016/j.str.2017.07.015

Jain V, Yogavel M, Oshima Y, Kikuchi H, Touquet B, Hakimi MA, et al. Structure of Prolyl-tRNA Synthetase-Halofuginone Complex Provides Basis for Development of Drugs against Malaria and Toxoplasmosis. Structure. 2015 May; 23 (5):819–29. DOI: https://doi.org/10.1016/j.str.2015.02.011

Son J, Lee EH, Park M, Kim JH, Kim J, Kim S, et al. Conformational changes in human prolyl-tRNA synthetase upon binding of the substrates proline and ATP and the inhibitor halofuginone. Acta Crystallogr D Biol Crystallogr. 2013 Oct; 69 (Pt 10):2136–45. DOI: https://doi.org/10.1107/S0907444913020556

Hewitt SN, Dranow DM, Horst BG, Abendroth JA, Forte B, Hallyburton I, et al. Biochemical and Structural Characterization of Selective Allosteric Inhibitors of the Plasmodium falciparum Drug Target, Prolyl-tRNA-synthetase. ACS Infect Dis. 2017 Jan; 3 (1):34–44.

Nyamai DW, Tastan Bishop Ö. Identification of Selective Novel Hits against Plasmodium falciparum Prolyl tRNA Synthetase Active Site and a Predicted Allosteric Site Using in silico Approaches. Int J Mol Sci. 2020 May; 21 (11). DOI: https://doi.org/10.3390/ijms21113803

Sterling T, Irwin JJ. ZINC 15 – Ligand Discovery for Everyone. J Chem Inf Model [Internet]. 2015 Nov 23 cited 2015; 55 (11):2324–37. Available from: https://doi.org/10.1021/acs.jcim.5b00559 DOI: https://doi.org/10.1021/acs.jcim.5b00559

Sunseri J, Koes DR. Pharmit: interactive exploration of chemical space. Nucleic Acids Res. 2016 Jul; 44 (W1):W442-8. DOI: https://doi.org/10.1093/nar/gkw287

Lipinski CA, Lombardo F, Dominy BW, Feeney PJ. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev [Internet]. 1997 cited 1997; 23 (1):3–25. Available from: https://www.sciencedirect.com/science/article/pii/S0169409X96004231 DOI: https://doi.org/10.1016/S0169-409X(96)00423-1

Lagorce D, Bouslama L, Becot J, Miteva MA, Villoutreix BO. FAF-Drugs4: free ADME-tox filtering computations for chemical biology and early stages drug discovery. Bioinformatics. 2017 Nov; 33 (22):3658–60. DOI: https://doi.org/10.1093/bioinformatics/btx491

Baell JB, Holloway GA. New Substructure Filters for Removal of Pan Assay Interference Compounds (PAINS) from Screening Libraries and for Their Exclusion in Bioassays. J Med Chem [Internet]. 2010 Apr 8 cited 2010; 53 (7):2719–40. Available from: https://doi.org/10.1021/jm901137j DOI: https://doi.org/10.1021/jm901137j

Maier JA, Martinez C, Kasavajhala K, Wickstrom L, Hauser KE, Simmerling C. ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB. J Chem Theory Comput [Internet]. 2015 Aug 11 cited 2015; 11 (8):3696–713. Available from:

https://doi.org/10.1021/acs.jctc.5b00255 DOI: https://doi.org/10.1021/acs.jctc.5b00255

Gasteiger J, Marsili M. Iterative partial equalization of orbital electronegativity—a rapid access to atomic charges. Tetrahedron [Internet]. 1980 cited 1980; 36 (22):3219–28. Available from: https://www.sciencedirect.com/science/article/pii/0040402080801682 DOI: https://doi.org/10.1016/0040-4020(80)80168-2

Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, et al. UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem. 2004 Oct; 25 (13):1605–12. DOI: https://doi.org/10.1002/jcc.20084

Raček T, Schindler O, Toušek D, Horský V, Berka K, Koča J, et al. Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges. Nucleic Acids Res [Internet]. 2020 Jul 2 cited 2020; 48 (W1):W591–6. Available from:

https://doi.org/10.1093/nar/gkaa367 DOI: https://doi.org/10.1093/nar/gkaa367

Kramer B, Rarey M, Lengauer T. Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking. Proteins. 1999 Nov; 37 (2):228–41. DOI: https://doi.org/10.1002/(SICI)1097-0134(19991101)37:2<228::AID-PROT8>3.0.CO;2-8

Triballeau N, Acher F, Brabet I, Pin JP, Bertrand HO. Virtual screening workflow development guided by the “receiver operating characteristic” curve approach. Application to high-throughput docking on metabotropic glutamate receptor subtype 4. J Med Chem. 2005 Apr; 48 (7):2534–47. DOI: https://doi.org/10.1021/jm049092j

Truchon JF, Bayly CI. Evaluating Virtual Screening Methods: Good and Bad Metrics for the “Early Recognition” Problem. J Chem Inf Model [Internet]. 2007 Mar 1 cited 2007; 47 (2):488–508. Available from: https://doi.org/10.1021/ci600426e DOI: https://doi.org/10.1021/ci600426e

Bura E, Gastwirth JL. The Binary Regression Quantile Plot: Assessing the Importance of Predictors in Binary Regression Visually. Biometrical J [Internet]. 2001 Feb 1 cited 2001; 43 (1):5–21. Available from: https://doi.org/10.1002/1521- 4036(200102)43:1%3C5::AID-BIMJ5%3E3.0.CO DOI: https://doi.org/10.1002/1521-4036(200102)43:1<5::AID-BIMJ5>3.0.CO;2-6

Empereur-Mot C, Zagury JF, Montes M. Screening Explorer–An Interactive Tool for the Analysis of Screening Results. J Chem Inf Model [Internet]. 2016 Dec 27 cited 2016; 56 (12):2281–6. Available from: https://doi.org/10.1021/acs.jcim.6b00283 DOI: https://doi.org/10.1021/acs.jcim.6b00283

Abraham MJ, Murtola T, Schulz R, Páll S, Smith JC, Hess B, et al. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX [Internet]. 2015 cited 2015; 1–2:19–25. Available from: https://www.sciencedirect.com/science/article/pii/S2352711015000059 DOI: https://doi.org/10.1016/j.softx.2015.06.001

Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. jcp. 1983 Jul; 79 (2):926–35. DOI: https://doi.org/10.1063/1.445869

Izadi S, Aguilar B, Onufriev A V. Protein–Ligand Electrostatic Binding Free Energies from Explicit and Implicit Solvation. J Chem Theory Comput [Internet]. 2015 Sep 8 cited 2015; 11 (9):4450–9. Available from: https://doi.org/10.1021/acs.jctc.5b00483 DOI: https://doi.org/10.1021/acs.jctc.5b00483

Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG. A smooth particle mesh Ewald method. J Chem Phys [Internet]. 1995 Nov 15 cited 1995; 103 (19):8577–93. Available from:

https://doi.org/10.1063/1.470117 DOI: https://doi.org/10.1063/1.470117

Bussi G, Donadio D, Parrinello M. Canonical sampling through velocity rescaling. J Chem Phys [Internet]. 2007 Jan 3 cited 2007; 126 (1):14101. Available from: https://doi.org/10.1063/1.2408420 DOI: https://doi.org/10.1063/1.2408420

Parrinello M, Rahman A. Polymorphic transitions in single crystals: A new molecular dynamics method. J Appl Phys [Internet]. 1981 Dec 1 cited 1981; 52 (12):7182–90. Available from:

https://doi.org/10.1063/1.328693 DOI: https://doi.org/10.1063/1.328693

42. Kumari R, Kumar R, Lynn A. g_mmpbsa—A GROMACS Tool for High-Throughput MM-PBSA Calculations. J Chem Inf Model [Internet]. 2014 Jul 28 cited 2014; 54 (7):1951–62. Available from: https://doi.org/10.1021/ci500020m DOI: https://doi.org/10.1021/ci500020m

Trager W, Jensen JB. Human malaria parasites in continuous culture. Science. 1976 Aug; 193 (4254):673–5. DOI: https://doi.org/10.1126/science.781840

Khasanah U, WidyaWaruyanti A, Hafid AF, Tanjung M. Antiplasmodial Activity of Isolated Polyphenols from Alectryon serratus Leaves Against 3D7 Plasmodium falciparum. Pharmacognosy Res. 2017 Dec; 9 (Suppl 1):S57–60. DOI: https://doi.org/10.4103/pr.pr_39_17

Kumar A, Zhang KYJ. Hierarchical virtual screening approaches in small molecule drug discovery. Methods. 2015 Jan; 71:26–37. DOI: https://doi.org/10.1016/j.ymeth.2014.07.007

Réau M, Langenfeld F, Zagury JF, Lagarde N, Montes M. Decoys Selection in Benchmarking Datasets: Overview and Perspectives [Internet]. Vol. 9, Frontiers in Pharmacology. 2018 cited 2018; Available from: https://www.frontiersin.org/articles/10.3389/fphar.2018.00011 DOI: https://doi.org/10.3389/fphar.2018.00011

47. Xing J, Li Q, Zhang S, Liu H, Zhao L, Cheng H, et al. Identification of dipeptidyl peptidase IV inhibitors: virtual screening, synthesis and biological evaluation. Chem Biol Drug Des. 2014 Sep; 84 (3):364–77. DOI: https://doi.org/10.1111/cbdd.12327

Al-Sha’er MA, Basheer HA, Taha MO. Discovery of new PKN2 inhibitory chemotypes via QSAR-guided selection of docking-based pharmacophores. Mol Divers. 2023 Feb; 27 (1):443–62. DOI: https://doi.org/10.1007/s11030-022-10434-4

Fawcett T. An introduction to ROC analysis. Pattern Recognit Lett. 2006; 27 (8):861–74. DOI: https://doi.org/10.1016/j.patrec.2005.10.010

Empereur-Mot C, Guillemain H, Latouche A, Zagury JF, Viallon V, Montes M. Predictiveness curves in virtual screening [Internet]. Vol. 7, Journal of cheminformatics. Laboratoire Génomique Bioinformatique et Applications, EA 4627, Conservatoire National des Arts et Métiers, 292 rue Saint Martin, 75003 Paris, France.; 2015 cited 2015; p. 52. Available from: DOI: https://doi.org/10.1186/s13321-015-0100-8

http://europepmc.org/abstract/MED/26539250

Thomsen R, Christensen MH. MolDock: A New Technique for High-Accuracy Molecular Docking. J Med Chem [Internet]. 2006 Jun 1 cited 2006; 49 (11):3315–21. Available from:

https://doi.org/10.1021/jm051197e DOI: https://doi.org/10.1021/jm051197e

Feher M. Consensus scoring for protein-ligand interactions. Drug Discov Today. 2006 May; 11 (9–10):421–8. DOI: https://doi.org/10.1016/j.drudis.2006.03.009

Humphrey W, Dalke A, Schulten K. VMD: Visual molecular dynamics. J Mol Graph [Internet]. 1996 cited 1996; 14 (1):33–8. Available from: DOI: https://doi.org/10.1016/0263-7855(96)00018-5

https://www.sciencedirect.com/science/article/pii/0263785596000185

Genheden S, Ryde U. The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opin Drug Discov. 2015 May; 10 (5):449–61. DOI: https://doi.org/10.1517/17460441.2015.1032936

Poli G, Granchi C, Rizzolio F, Tuccinardi T. Application of MM-PBSA Methods in Virtual Screening. Molecules. 2020 Apr; 25 (8). DOI: https://doi.org/10.3390/molecules25081971

King E, Aitchison E, Li H, Luo R. Recent Developments in Free Energy Calculations for Drug Discovery [Internet]. Vol. 8, Frontiers in Molecular Biosciences. 2021 cited 2021; Available from: DOI: https://doi.org/10.3389/fmolb.2021.712085

https://www.frontiersin.org/articles/10.3389/fmolb.2021.712085

Bhatt TK, Kapil C, Khan S, Jairajpuri MA, Sharma V, Santoni D, et al. A genomic glimpse of aminoacyl-tRNA synthetases in malaria parasite Plasmodium falciparum. BMC Genomics [Internet]. 2009 cited 2009; 10 (1):644. Available from: https://doi.org/10.1186/1471-2164-10-644 DOI: https://doi.org/10.1186/1471-2164-10-644