478
Views
9
CrossRef citations to date
0
Altmetric
Research Articles

Evaluation of potential drugs against leishmaniasis targeting catalytic subunit of Leishmania donovani nuclear DNA primase using ligand based virtual screening, docking and molecular dynamics approaches

, , , , &
Pages 1838-1852 | Received 15 Jan 2020, Accepted 02 Mar 2020, Published online: 17 Mar 2020

References

  • Abdelli, I., Benariba, N., Adjdir, S., Fekhikher, Z., Daoud, I., Terki, M., Benramdane, H., & Ghalem, S. (2020). In silico evaluation of phenolic compounds as inhibitors of α-amylase and α-glucosidase. Journal of Biomolecular Structure and Dynamics, 1–13. 10.1080/07391102.2020.1718553.
  • Agarwal, A., Louise-May, S., Thanassi, J. A., Podos, S. D., Cheng, J., Thoma, C., Liu, C., Wiles, J. A., Nelson, D. M., Phadke, A. S., Bradbury, B. J., Deshpande, M. S., & Pucci, M. J. (2007). Small molecule inhibitors of E. coli primase, a novel bacterial target. Bioorganic & Medicinal Chemistry Letters, 17(10), 2807–2810. doi:10.1016/j.bmcl.2007.02.056
  • Alvar, J., Bashaye, S., Argaw, D., Cruz, I., Aparicio, P., Kassa, A., Orfanos, G., Parreño, F., Babaniyi, O., Gudeta, N., Cañavate, C., & Bern, C. (2007). Kala-azar outbreak in Libo Kemkem, Ethiopia: Epidemiologic and parasitologic assessment. The American Journal of Tropical Medicine and Hygiene, 77(2), 275–282. doi:10.4269/ajtmh.2007.77.275
  • Amin, M. L. (2013). P-glycoprotein inhibition for optimal drug delivery. Drug Target Insights, 7, DTI.S12519. doi:10.4137/DTI.S12519
  • Arezi, B., & Kuchta, R. D. (2000). Eukaryotic DNA primase. Trends in Biochemical Sciences, 25(11), 572–576. doi:10.1016/s0968-0004(00)01680-7
  • Azam, S. S., Sarfaraz, S., & Abro, A. (2014). Comparative modeling and virtual screening for the identification of novel inhibitors for myo-inositol-1-phosphate synthase. Molecular Biology Reports, 41(8), 5039–5052. doi:10.1007/s11033-014-3370-8
  • Banerjee, P., Eckert, A. O., Schrey, A. K., & Preissner, R. (2018). ProTox-II: A webserver for the prediction of toxicity of chemicals. Nucleic Acids Research, 46(W1), W257–W263. doi:10.1093/nar/gky318
  • Baranovskiy, A. G., Zhang, Y., Suwa, Y., Babayeva, N. D., Gu, J., Pavlov, Y. I., & Tahirov, T. H. (2015). Crystal structure of the human primase. Journal of Biological Chemistry, 290(9), 5635–5646. doi:10.1074/jbc.M114.624742
  • Biswas, T., Green, K. D., Garneau-Tsodikova, S., & Tsodikov, O. V. (2013). Discovery of Inhibitors of Bacillus anthracis primase DnaG. Biochemistry, 52(39), 6905–6910. doi:10.1021/bi4011286
  • Brochu, C., Haimeur, A., & Ouellette, M. (2004). The heat shock protein HSP70 and heat shock cognate protein HSC70 contribute to antimony tolerance in the protozoan parasite Leishmania. Cell Stress & Chaperones, 9(3), 294–303. doi:10.1379/CSC-15R1.1
  • Chakrabarti, S., & Lanczycki, C. J. (2007). Analysis and prediction of functionally important sites in proteins. Protein Science, 16(1), 4–13. doi:10.1110/ps.062506407
  • Chandrasekaran, K., & Thilak Kumar, R. (2016). Molecular properties prediction, docking studies and antimicrobial screening of ornidazole and its derivatives. Journal of Chemical and Pharmaceutical Research, 8(3), 849–861.
  • Chawla, B., & Madhubala, R. (2010). Drug targets in Leishmania. Journal of Parasitic Diseases, 34(1), 1–13. doi:10.1007/s12639-010-0006-3
  • Coelho, A. C., Beverley, S. M., & Cotrim, P. C. (2003). Functional genetic identification of PRP1, an ABC transporter superfamily member conferring pentamidine resistance in Leishmania major. Molecular and Biochemical Parasitology, 130(2), 83–90. doi:10.1016/S0166-6851(03)00162-2
  • Colovos, C., & Yeates, T. O. (1993). Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Science, 2(9), 1511–1519. doi:10.1002/pro.5560020916
  • Copeland, W. C., & Tan, X. (1995). Active site mapping of the catalytic mouse primase subunit by alanine scanning mutagenesis. Journal of Biological Chemistry, 270(8), 3905–3913. doi:10.1074/jbc.270.8.3905
  • Dallakyan, S., & Olson, A. J. (2014). Small-molecule library screening by docking with PyRx. Chemical Biology, 1263, 243–250. doi:10.1007/978-1-4939-2269-7_19.
  • Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98(12), 10089–10092. doi:10.1063/1.464397
  • Decuypere, S., Rijal, S., Yardley, V., De Doncker, S., Laurent, T., Khanal, B., Chappuis, F., & Dujardin, J.-C. (2005). Gene expression analysis of the mechanism of natural Sb(V) resistance in Leishmania donovani isolates from Nepal. Antimicrobial Agents and Chemotherapy, 49(11), 4616–4621. doi:10.1128/AAC.49.11.4616-4621.2005
  • Egan, W. J., Merz, K. M., & Baldwin, J. J. (2000). Prediction of drug absorption using multivariate statistics. Journal of Medicinal Chemistry, 43(21), 3867–3877. doi:10.1021/jm000292e
  • Eisenberg, D., Lüthy, R., & Bowie, J. U. (1997). VERIFY3D: Assessment of protein models with three-dimensional profiles. Macromolecular Crystallography Part B, 20, 396–404. 10.1016/s0076-6879(97)77022-8.
  • Ghorbani, M., & Farhoudi, R. (2017). Leishmaniasis in humans: Drug or vaccine therapy? Drug Design, Development and Therapy, 12, 25–40. doi:10.2147/DDDT.S146521
  • Gleeson, M. P. (2008). Generation of a set of simple, interpretable ADMET rules of thumb. Journal of Medicinal Chemistry, 51(4), 817–834. doi:10.1021/jm701122q
  • González, U., Pinart, M., Reveiz, L., Rengifo‐Pardo, M., Tweed, J., Macaya, A., & Alvar, J. (2010). Designing and reporting clinical trials on treatments for cutaneous leishmaniasis. Clinical Infectious Diseases, 51(4), 409–419. doi:10.1086/655134
  • Guilliam, T. A., Keen, B. A., Brissett, N. C., & Doherty, A. J. (2015). Primase-polymerases are a functionally diverse superfamily of replication and repair enzymes. Nucleic Acids Research, 43(14), 6651–6664. doi:10.1093/nar/gkv625
  • Guilliam, T. A., & Doherty, A. J. (2017). Current and emerging assays for studying the primer synthesis activities of DNA primases. Methods in Enzymology, 591, 327–353. doi:10.1016/bs.mie.2017.03.006.
  • Hakeem, S., Singh, I., Sharma, P., Verma, V., & Chandra, R. (2019). in silico screening and molecular dynamics simulations study to identify novel potent inhibitors against Mycobacterium tuberculosis DnaG primase. Acta Tropica, 199, 105154. doi:10.1016/j.actatropica.2019.105154
  • Hertz-Fowler, C., & Peacock, C. S. (2002). Introducing GeneDB: A generic database. Trends in Parasitology, 18(10), 465–467. doi:10.1016/S1471-4922(02)02361-9
  • Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. doi:10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
  • Hodge, A., Sterner, B. (2005). Toxicity classes. Canadian Center for Occupational Health and Safety. [Cited 2017 August 4]. https://www.ccohs.ca/oshanswers/chemicals/id50.htm
  • Iyer, L. M. (2005). Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: Structural insights and new members. Nucleic Acids Research, 33(12), 3875–3896. doi:10.1093/nar/gki702
  • James, S., Larson, K., Acosta, E., & Prichard, M. (2014). Helicase-primase as a target of new therapies for herpes simplex virus infections. Clinical Pharmacology & Therapeutics, 97(1), 66–78. doi:10.1002/cpt.3
  • Jerônimo, S. M., & Pearson, R. D. (2016). The challenges on developing vaccine against visceral leishmaniasis. Revista da Sociedade Brasileira de Medicina Tropical, 49(4), 395–397. doi:10.1590/0037-8682-0343-2016
  • Jeyaram, R. A., Priyadarzini, T. R. K., Radha, C. A., Shanmugam, N. R. S., Ramakrishnan, C., Gromiha, M. M., & Veluraja, K. (2019). Molecular dynamics simulation studies on influenza A virus H5N1 complexed with sialic acid and fluorinated sialic acid. Journal of Biomolecular Structure and Dynamics, 37, 4813–4824. doi:10.1080/07391102.2019.1568304
  • Kuldeep, J., Pavneet Kaur, K. R., Goyal, N., & ImranSiddiqi, M. (2020). Identification of potential anti-leishmanial agents using computational investigationand biological evaluation against Trypanothione reductase. Journal of Biomolecular Structure and Dynamics, 1–10. 10.1080/07391102.2020.1721330.
  • Joshi, T., Joshi, T., Sharma, P., Chandra, S., & Pande, V. (2020). Molecular docking and molecular dynamics simulation approach to screen natural compounds for inhibition of Xanthomonas oryzae pv. Oryzae by targeting Peptide Deformylase. Journal of Biomolecular Structure and Dynamics, 1–18. 10.1080/07391102.2020.1719200.
  • Kamhawi, S. (2006). Phlebotomine sand flies and Leishmania parasites: Friends or foes? Trends in Parasitology, 22(9), 439–445. doi:10.1016/j.pt.2006.06.012
  • Kashif, M., Manna, P. P., Akhter, Y., Alaidarous, M., & Rub, A. (2017). Screening of novel inhibitors against Leishmania donovani Calcium ion channel to fight Leishmaniasis. Infect Disorders - Drug Targets, 17(2), 120–129. doi:10.2174/1871526516666161230124513.
  • Knyazev, A. V., & Lashuk, I. (2008). Steepest descent and conjugate gradient methods with variable preconditioning. SIAM Journal on Matrix Analysis and Applications, 29(4), 1267–1280. doi:10.1137/060675290
  • Krieger, E., Joo, K., Lee, J., Lee, J., Raman, S., Thompson, J., Tyka, M., Baker, D., & Karplus, K. (2009). Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8. Proteins: Structure, Function, and Bioinformatics, 77(S9), 114–122. doi:10.1002/prot.22570
  • Kuron, A., Korycka-Machala, M., Brzostek, A., Nowosielski, M., Doherty, A., Dziadek, B., & Dziadek, J. (2014). Evaluation of DNA primase DnaG as a potential target for antibiotics. Antimicrobial Agents and Chemotherapy, 58(3), 1699–1706. doi:10.1128/AAC.01721-13
  • Kwofie, S. K., Enninful, K. S., Yussif, J. A., Asante, L. A., Adjei, M., Kan-Dapaah, K., Tiburu, E. K., Mensah, W. A., Miller, W. A., Mosi, L., & Wilson, M. D. (2019). Molecular informatics studies of the iron-dependent regulator (ideR) reveal potential novel anti-mycobacterium ulcerans natural product-derived compounds. Molecules, 24(12), 2299. doi:10.3390/molecules24122299
  • Lagorce, D., Bouslama, L., Becot, J., Miteva, M. A., & Villoutreix, B. O. (2017). FAF-Drugs4: Free ADME-tox filtering computations for chemical biology and early stages drug discovery. Bioinformatics, 33(22), 3658–3660. doi:10.1093/bioinformatics/btx491
  • Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993). PROCHECK: A program to check the stereochemical quality of protein structures. Journal of Applied Crystallography, 26(2), 283–291. doi:10.1107/S0021889892009944
  • Li, W.-Y., Duan, Y.-Q., Lu, X.-H., Ma, Y., & Wang, R.-L. (2019). Exploring the cause of the inhibitor 4AX attaching to binding site disrupting protein tyrosine phosphatase 4A1 trimerization by molecular dynamic simulation. Journal of Biomolecular Structure and Dynamics, 37, 4840–4851. doi:10.1080/07391102.2019.1567392
  • Liao, K. H., Chen, K.-B., Lee, W.-Y., Sun, M.-F., Lee, C.-C., & Chen, C. Y.-C. (2014). Ligand-based and structure-based investigation for Alzheimer’s disease from traditional Chinese medicine. Evidence-Based Complementary and Alternative Medicine, 2014, 1–16. doi:10.1155/2014/364819
  • Lill, M. A., & Danielson, M. L. (2011). Computer-aided drug design platform using PyMOL. Journal of Computer-Aided Molecular Design, 25(1), 13–19. doi:10.1007/s10822-010-9395-8
  • Lipinski, C. A. (2004). Lead- and drug-like compounds: The rule-of-five revolution. Drug Discovery Today: Technologies, 1(4), 337–341. doi:10.1016/j.ddtec.2004.11.007
  • Logan-Klumpler, F. J., De Silva, N., Boehme, U., Rogers, M. B., Velarde, G., McQuillan, J. A., Carver, T., Aslett, M., Olsen, C., Subramanian, S., Phan, I., Farris, C., Mitra, S., Ramasamy, G., Wang, H., Tivey, A., Jackson, A., Houston, R., Parkhill, J., … Berriman, M. (2012). GeneDB–an annotation database for pathogens. Nucleic Acids Research, 40(D1), D98–D108. doi:10.1093/nar/gkr1032
  • Makesh Raj L. S., Jude, J., Kannan, I., Sai Krishna, P., & Shankar, K. A. (2014). Molecular docking study for inhibitors of Aggregatibacter actinomycetamcomitans toxins in treatment of aggressive perioodontitis. Journal of Clinical and Diagnostic Research, 8(11), ZC48-51. doi:10.7860/JCDR/2014/10067.5133
  • Malathi, K., Anbarasu, A., & Ramaiah, S. (2019). Identification of potential inhibitors for Klebsiella pneumoniae carbapenemase-3: A molecular docking and dynamics study. Journal of Biomolecular Structure and Dynamics, 37, 4601–4613. doi:10.1080/07391102.2018.1556737
  • Malde, A. K., Zuo, L., Breeze, M., Stroet, M., Poger, D., Nair, P. C., Oostenbrink, C., & Mark, A. E. (2011). An automated force field topology builder (ATB) and repository: Version 1.0. Journal of Chemical Theory and Computation, 7(12), 4026–4037. doi:10.1021/ct200196m
  • Maltezou, H. C. (2010). Drug resistance in visceral leishmaniasis. Journal of Biomedicine and Biotechnology, 2010, 1–8. doi:10.1155/2010/617521
  • Martin, Y. C. (2005). A bioavailability score. Journal of Medicinal Chemistry, 48(9), 3164–3170. doi:10.1021/jm0492002
  • Mbongo, N., Loiseau, P. M., Billion, M. A., & Robert-Gero, M. (1998). Mechanism of amphotericin B resistance in Leishmania donovani promastigotes. Antimicrobial Agents and Chemotherapy, 42(2), 352–357. 10.1128/AAC.42.2.352.
  • McCall, L.-I., Zhang, W.-W., & Matlashewski, G. (2013). Determinants for the development of visceral leishmaniasis disease. PLoS Pathogens, 9(1), e1003053. doi:10.1371/journal.ppat.1003053
  • Mizuno, T., Okamoto, T., Yokoi, M., Izumi, M., Kobayashi, A., Hachiya, T., Tamai, K., Inoue, T., & Hanaoka, F. (1996). Identification of the nuclear localization signal of mouse DNA primase: Nuclear transport of p46 subunit is facilitated by interaction with p54 subunit. Journal of Cell Science, 109(11), 2627–2636.
  • Mokhnache, K., Madoui, S., Khither, H., & Charef, N. (2019). Drug-likeness and pharmacokinetics of a bis-phenolic ligand: Evaluations by computational methods. Scholars Journal of Applied Medical Sciences, 7(1), 167–173. 10.21276/sjams.2019.7.1.31.
  • Murray, H. W., Berman, J. D., Davies, C. R., & Saravia, N. G. (2005). Advances in leishmaniasis. The Lancet, 366(9496), 1561–1577. doi:10.1016/S0140-6736(05)67629-5
  • Nisha, C. M., Kumar, A., Nair, P., Gupta, N., Silakari, C., Tripathi, T., & Kumar, A. (2016). Molecular docking and in silico ADMET study reveals acylguanidine 7a as a potential inhibitor of β-secretase. Advances in Bioinformatics, 2016, 1–6. doi:10.1155/2016/9258578
  • Paine, S. W., Barton, P., Bird, J., Denton, R., Menochet, K., Smith, A., Tomkinson, N. P., & Chohan, K. K. (2010). A rapid computational filter for predicting the rate of human renal clearance. Journal of Molecular Graphics and Modelling, 29(4), 529–537. doi:10.1016/j.jmgm.2010.10.003
  • Perez-Victoria, J. M., Parodi-Talice, A., Torres, C., Gamarro, F., & Castanys, S. (2001). ABC transporters in the protozoan parasite Leishmania. International Microbiology, 4(3), 159–166. doi:10.1007/s10123-001-0031-2
  • Pinto-Martinez, A. K., Rodriguez-Durán, J., Serrano-Martin, X., Hernandez-Rodriguez, V., & Benaim, G. (2017). Mechanism of action of miltefosine on Leishmania donovani involves the impairment of acidocalcisome function and the activation of the sphingosine-dependent plasma membrane Ca 2+ channel. Antimicrobial Agents and Chemotherapy, 62(1), e01614-17. doi:10.1128/AAC.01614-17
  • Pires, D. E. V., Blundell, T. L., & Ascher, D. B. (2015). pkCSM: Predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures. Journal of Medicinal Chemistry, 58(9), 4066–4072. doi:10.1021/acs.jmedchem.5b00104
  • Raies, A. B., & Bajic, V. B. (2016). In silico toxicology: Computational methods for the prediction of chemical toxicity. Wiley Interdisciplinary Reviews: Computational Molecular Science, 6(2), 147–172. doi:10.1002/wcms.1240
  • Šali, A., Potterton, L., Yuan, F., van Vlijmen, H., & Karplus, M. (1995). Evaluation of comparative protein modeling by MODELLER. Proteins: Structure, Function, and Genetics, 23(3), 318–326. doi:10.1002/prot.340230306
  • Shahraki, O., Zargari, F., Edraki, N., Khoshneviszadeh, M., Firuzi, O., & Miri, R. (2017). Molecular dynamics simulation and molecular docking studies of 1,4-dihydropyridines as P-glycoprotein’s allosteric inhibitors. Journal of Biomolecular Structure and Dynamics, 36(1), 112–125. doi:10.1080/07391102.2016.1268976
  • Shang, J., Dai, X., Li, Y., Pistolozzi, M., & Wang, L. (2017). HybridSim-VS: A web server for large-scale ligand-based virtual screening using hybrid similarity recognition techniques. Bioinformatics, 33(21), 3480–3481. doi:10.1093/bioinformatics/btx418
  • Shanmugam, A., & Natarajan, J. (2012). Comparative modeling of UDP-N-acetylmuramoyl-glycyl-D-glutamate-2, 6-diaminopimelate ligase from Mycobacterium leprae and analysis of its binding features through molecular docking studies. Journal of Molecular Modeling, 18(1), 115–125. doi:10.1007/s00894-011-1039-y
  • Sievers, F., Wilm, A., Dineen, D., Gibson, T. J., Karplus, K., Li, W., Lopez, R., McWilliam, H., Remmert, M., Söding, J., Thompson, J. D., & Higgins, D. G. (2011). Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology, 7(1), 539. doi:10.1038/msb.2011.75
  • Singh, N., Kumar, M., & Singh, R. K. (2012). Leishmaniasis: Current status of available drugs and new potential drug targets. Asian Pacific Journal of Tropical Medicine , 5(6), 485–497. doi:10.1016/S1995-7645(12)60084-4
  • Sood, D., Kumar, N., Singh, A., Sakharkar, M. K., Tomar, V., & Chandra, R. (2018). Antibacterial and pharmacological evaluation of fluoroquinolones: A chemoinformatics approach. Genomics & Informatics, 16(3), 44–51. doi:10.5808/GI.2018.16.3.44
  • Srimai, V., Ramesh, M., Satya Parameshwar, K., & Parthasarathy, T. (2013). Computer-aided design of selective Cytochrome P450 inhibitors and docking studies of alkyl resorcinol derivatives. Medicinal Chemistry Research, 22(11), 5314–5323. doi:10.1007/s00044-013-0532-5
  • Suvannang, N., Nantasenamat, C., Isarankura-Na-Ayudhya, C., & Prachayasittikul, V. (2011). Molecular docking of aromatase inhibitors. Molecules, 16(5), 3597–3617. doi:10.3390/molecules16053597
  • Syed, S. B., Arya, H., Fu, I.-H., Yeh, T.-K., Periyasamy, L., Hsieh, H.-P., & Coumar, M. S. (2017). Targeting P-glycoprotein: Investigation of piperine analogs for overcoming drug resistance in cancer. Scientific Reports, 7(1), 1–18. doi:10.1038/s41598-017-08062-2
  • Tamiya-Koizumi, K., Murate, T., Suzuki, M., Simbulan, C. M., Nakagawa, M., Takemura, M., Furuta, K., Izuta, S., & Yoshida, S. (1997). Inhibition of DNA primase by sphingosine and its analogues parallels with their growth suppression of cultured human leukemic cells. IUBMB Life, 41(6), 1179–1189. doi:10.1080/15216549700202271
  • Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. C. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718. doi:10.1002/jcc.20291
  • Veber, D. F., Johnson, S. R., Cheng, H.-Y., Smith, B. R., Ward, K. W., & Kopple, K. D. (2002). Molecular properties that influence the oral bioavailability of drug candidates. Journal of Medicinal Chemistry, 45(12), 2615–2623. doi:10.1021/jm020017n
  • Wallace, A. C., Laskowski, R. A., & Thornton, J. M. (1995). LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Protein Engineering, Design and Selection, 8(2), 127–134. doi:10.1093/protein/8.2.127
  • Wang, H., Dommert, F., & Holm, C. (2010). Optimizing working parameters of the smooth particle mesh Ewald algorithm in terms of accuracy and efficiency. The Journal of Chemical Physics, 133(3), 034117. doi:10.1063/1.3446812
  • Wang, Z., Hop, C. E. C. A., Leung, K. H., & Pang, J. (2000). Determination of in vitro permeability of drug candidates through a Caco-2 cell monolayer by liquid chromatography/tandem mass spectrometry. Journal of Mass Spectrometry, 35(1), 71–76. doi:10.1002/(SICI)1096-9888(200001)35:1<71::AID-JMS915>3.0.CO;2-5
  • Wiederstein, M., & Sippl, M. J. (2007). ProSA-web: Interactive web service for the recognition of errors in three dimensional structures of proteins. Nucleic Acids Research, 35(Web Server), W407–W410. doi:10.1093/nar/gkm290
  • Yang, J., Roy, A., & Zhang, Y. (2013). Protein–ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment. Bioinformatics, 29(20), 2588–2595. doi:10.1093/bioinformatics/btt447
  • Yang, J.-M., & Chen, C.-C. (2004). GEMDOCK: A generic evolutionary method for molecular docking. Proteins: Structure, Function, and Bioinformatics, 55(2), 288–304. doi:10.1002/prot.20035
  • Ye, J., McGinnis, S., & Madden, T. L. (2006). BLAST: Improvements for better sequence analysis. Nucleic Acids Research, 34(Web Server), W6–W9. doi:10.1093/nar/gkl164
  • Yoshida, F., & Topliss, J. G. (2000). QSAR model for drug human oral bioavailability1. Journal of Medicinal Chemistry, 43(13), 2575–2585. doi:10.1021/jm0000564
  • Zafar, R., Zubair, M., Ali, S., Shahid, K., Waseem, W., Naureen, H., Haider, A., Jan, M. S., Ullah, F., Sirajuddin, M., & Sadiq, A. (2020). Zinc metal carboxylates as potential anti-Alzheimer’s candidate: In-vitro anticholinesterase, antioxidant and molecular docking studies. Journal of Biomolecular Structure and Dynamics, 1–15. 10.1080/07391102.2020.1724569.
  • Zerbe, L. K., & Kuchta, R. D. (2002). The p58 subunit of human DNA primase is important for primer initiation, elongation, and counting†. Biochemistry, 41(15), 4891–4900. doi:10.1021/bi016030b
  • Zhang, C., Freddolino, P. M., & Zhang, Y. (2017). COFACTOR: Improved protein function prediction by combining structure, sequence and protein-protein interaction information. Nucleic Acids Research, 45(W1), W291–W299. doi:10.1093/nar/gkx366
  • Zhang, L., McHale, C. M., Greene, N., Snyder, R. D., Rich, I. N., Aardema, M. J., Roy, S., Pfuhler, S., & Venkatactahalam, S. (2014). Emerging approaches in predictive toxicology. Environmental and Molecular Mutagenesis, 55(9), 679–688. doi:10.1002/em.21885
  • Zhang, X., Yan, J., Wang, H., Wang, Y., Wang, J., & Zhao, D. (2020). Molecular docking, 3D-QSAR, and molecular dynamics simulations of thieno[3,2-b]pyrrole derivatives against anticancer targets of KDM1A/LSD1. Journal of Biomolecular Structure and Dynamics, 1–14. 10.1080/07391102.2020.1726819.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.