Herbal Compound Screening with GPU Computation on ZINC Database through Similarity Comparison Approach
(1) Department of Computer Science, Faculty of Mathematics and Natural Sciences, IPB University
(2) Department of Computer Science, Faculty of Mathematics and Natural Sciences, IPB University Tropical Biophamarca Research Center, Institute of Research and Community Services, IPB University
(3) Department of Computer Science, Faculty of Mathematics and Natural Sciences, IPB University
(*) Corresponding Author
DOI: https://doi.org/10.23917/khif.v8i2.16349
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World Health Organization Indonesia, “Weekly Epidemiological Update on COVID-19,” World Health Organization Indonesia, Jakarta, Indonesia, 23 Jul. 2021.
C. G. Bologa, O. Ursu, and T. I. Oprea, “How to prepare a compound collection prior to virtual screening,” Methods in Molecular Biology, vol. 1939, pp. 119–138, 2019.
T. T. Ashburn and K. B. Thor, “Drug repositioning: Identifying and developing new uses for existing drugs,” Nature Reviews Drug Discovery, vol. 3, no. 8, pp. 673–683, 2004.
F. Medail and P. Quezel, “Biodiversity hotspots in the Mediterranean Basin: Setting global conservation priorities,” Conservation Biology, vol. 13, no. 6, pp. 1510–1513, 1999.
A. Athanasopoulos, A. Dimou, V. Mezaris, I. Kompatsiaris, Z. Wen, J. Shi, et al., “Performance of deep learning computation with TensorFlow software library in GPU-capable multi-core computing platforms,” in International Workshop on Image Analysis for Multimedia Service, vol. 19, pp. 240–242, 2017.
A. Reinaldo, W. A. Kusuma, H. Rahmawan, and Y. Herdiyeni, “Implementation of breadth-first search parallel to predict drug-target interaction in plant-disease graph,” in International Conference on Computer Science and Its Application in Agriculture (ICOSICA), pp. 1-5, 2020.
B. Imbernon, A. Serrano, A. Bueno-Crespo, J. L. Abellan, H. Perez-Sanchez, and J. M. Cecilia, “METADOCK 2: a high-throughput parallel metaheuristic scheme for molecular docking,” Bioinformatics, vol. 37, no. 11, pp. 1515-1520, 2021.
I. Sanchez-Linares, H. Perez-Sanchez, J. M. Cecilia, and J. M. Garcia, “High-throughput parallel blink virtual screening using BINDSURF,” BMC Bioinformatics, vol. 13, no. 14, pp. 1-14, 2012.
T. I. Oprea, C. G. Bologa, B. S. Edwards, E. R. Prossnitz, and L. A. Sklar, “Post-high-throughput screening analysis: An empirical compound prioritization scheme,” Journal of Biomolecular Screening, vol. 10, no. 5, pp. 419–426, 2005.
G. M. Rishton, “Reactive compounds and in vitro false positives in HTS,” Drug Discovery Today, vol. 2, no. 9, pp. 382–384, 1997.
G. M. Rishton, “Nonleadlikeness and leadlikeness in biochemical screening,” Drug Discovery Today, vol. 8, no. 2, pp. 86–96, 2003.
S. L. McGovern, E. Caselli, N. Grigorieff, and B. K. Shoichet, “A common mechanism underlying promiscuous inhibitors from virtual and high-throughput screening,” Journal of Medicinal Chemistry, vol 45, no. 8, pp. 1712–1722, 2002.
V. P. Kamboj, “Herbal medicine,” Current Science, vol. 78, no. 1, pp. 35-39, 2000.
S. K. Pal and Y. Shukla, “Herbal medicine: current status and the future,” Asian Pacific Journal of Cancer Prevention, vol. 4, no. 4, pp. 281-288, 2003.
P. Basnet and N. Skalko-Basnet “Curcumin: An anti-inflammatory molecule from a curry spice on the path to cancer treatment,” Molecules, vol. 16, no. 6, pp. 4567–4598, 2011.
D. Luebke, M. Harris, N. Govindaraju, A. Lefohn, M. Houston, J. Owens, et al., “GPGPU: general-purpose computation on graphics hardware,” in ACM/IEEE Conference on Supercomputing, 2006.
F. Li, Y. Ye, Z. Tian, and X. Zhang, “CPU versus GPU: which can perform matrix computation faster—performance comparison for basic linear algebra subprograms,” Neural Computing and Applications, vol. 31, no. 8, pp. 4353–4365, 2019.
NVIDIA Corporation, “CUDA Toolkit Documentation - v11.4.0,” NVIDIA Corporation, Santa Clara, United States, 2021.
J. J. Irwin, T. Sterling, M. M. Mysinger, E. S. Bolstad, and R. G. Coleman, “ZINC: a free tool to discover chemistry for biology,” Journal of Chemical Information and Modeling, vol. 52, no. 7, pp. 1757–1768, 2012.
F. Corpet, “Multiple sequence alignment with hierarchical clustering,” Nucleic Acids Research, vol. 16, no. 22, pp. 10881–10890, 1984.
D. Bajusz, A. Racz, and K. Heberger, “Why is Tanimoto index an appropriate choice for fingerprint-based similarity calculations?,” Journal of Cheminformatics, vol. 7, no. 1, pp. 1-13, 2015.
Y. C. Cao, Q. X. Deng, and S. X. Dai, “Remdesivir for severe acute respiratory syndrome coronavirus 2 causing COVID-19: An evaluation of the evidence,” Travel Medicine and Infectious Disease, vol. 35, pp. 101647, 2020.
Y. Furuta, T. Komeno, and T. Nakamuba, “Favipiravir (T-705), a broad spectrum inhibitor of viral RNA polymerase,” in Proceedings of the Japan Academy, Series B, vol. 93, no. 7, pp. 449–463, 2017.
R. S. Cvetkovic and K. L. Goa, “Lopinavir/Ritonavir”, Drugs, vol. 63, no. 8, pp. 769–802, 2003.
Z. N. Lei, Z. X. Wu, S. Dong, D-H. Yang, L. Zhang, Z. Ke, C. Zou, and Z-S. Chen, “Chloroquine and hydroxychloroquine in the treatment of malaria and repurposing in treating COVID-19,” Pharmacology & Therapeutics, vol. 216, no. 1, pp. 107672, 2020.
D. B. Mahmoud, Z. Shitu, and A. Mostafa, “Drug repurposing of nitazoxanide: can it be an effective therapy for COVID-19?,” Journal of Genetic Engineering and Biotechnology, vol. 18, no. 35, pp. 1–10, 2020.
A. Tan, L. Duan, Y. Ma, Q. Huang, K. Mao, W. Xiao, et al., “Is oseltamivir suitable for fighting against COVID-19: In silico assessment, in vitro and retrospective study,” Bioorganic Chemistry, vol. 104, pp. 104257, 2020.
T. F. de Koning-Ward, A. P. Waters, and S. Brendan, “Puromycin-N-acetyltransferase as a selectable marker for use in Plasmodium falciparum,” Molecular and Biochemical Parasitology, vol. 117, no. 2, pp. 155-160, 2001.
G. Lang, M. I. Mitova, G. Ellis, S. van der Sar, R. K. Phipps, J. W. Blunt, et al., “Bioactivity profiling using HPLC/microtiter-plate analysis: application to a New Zealand marine alga-derived fungus, Gliocladium sp.,” Journal of Natural Products, vol. 69, no. 4, pp. 621-624, 2006.
M. Isaka, S. Palasarn, S. Lapanun, and K. Sriklung, “Paecilodepsipeptide A, an antimalarial and antitumor cyclohexadepsipeptide from the insect pathogenic fungus Paecilomyces cinnamomeus BCC 9616,” Journal of Natural Products, vol. 70, no. 4, pp. 675-678, 2007.
S. R. Giacomelli, F. C. Missau, M. A. Mostardeiro, U. F. da Silva, I. I. Dalcol, N. Zanatta, and A. Morel, “Cyclopeptides from the bark of Disaria americana,” Journal of Natural Products, vol. 64, no. 7, pp. 997-999, 2001
A. G. Tolkushin, E. A. Luchinin, M. E. Kholovnya-Voloskova, and A. A. Zavyalov, “History of aminoquinoline preparations: from cinchona bark to chloroquine and hydroxychloroquinon,” Problemy Sotsial'noi Gigieny, Zdravookhraneniia i Istorii Meditsiny, vol. 28 [special issue], pp. 1118-1122, 2020.
R. Goto, K. Okura, H. Sakazaki, T. Sugawara, S. Matsuoka, and M. Inoue, “Synthesis and biological evaluation of triazole analogues of antillatoxin,” Tetrahedron, vol. 67, no. 35, pp. 6659-6672, 2011.
G. X. Zhou, E. K. Wijeratne, D. Bigelow, L. S. Pierson, H. D. VanEtten, and A. L. Gunatilaka, “Aspochalasins I, J, and K: three new cytotoxic cytochalasans of Aspergillus flavipes from the rhizosphere of Ericameria laricifolia of the Sonoran Desert,” Journal of Natural Products, vol. 67, no. 3, pp. 328-332, 2004.
Y. C. Shen, Y. B. Cheng, J. Kobayashi, T. Kubota, Y. Takahashi, Y. Mikami, et al., “Nitrogen-containing verticillene diterpenoids from the taiwanese soft coral Cespitularia taeniata,” Journal of Natural Products, vol. 70, no. 12, pp. 1961-1965, 2007.
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