The Structure-Based Virtual Screening for Natural Compounds that Bind with the Activating Receptors of Natural Killer Cells doi.org/10.26538/tjnpr/v5i1.21
Main Article Content
Abstract
The natural killer (NK) cells are responsible for immuno-surveillance against cancer and virally -infected cells. Ligand-binding with the activating receptors of the NK cells induces the tyrosine phosphorylation of the Immunoreceptor Tyrosine–based Activation Motif (ITAM) of adaptor proteins and triggers the direct cytotoxicity and the production of inflammatory cytokines through signal pathways. In this study, 1,697 natural compounds were obtained from 79 edible tropical plants through data mining. The in silico molecular docking simulations of these compounds were executed against 18 activating NK cell receptor targets using the Python Prescription (PyRx) 0.8 software incorporating both Vina and AutoDock 4.2 plug-in tools. An arbitrary docking score ≥ -7.0 kcal/mol was chosen as cut-off value. Further screening for ligand efficiency, drug-likeness, Absorption Distribution Metabolism Excretion and Toxicity (ADMET) properties, Pan Assay Interference Compounds (PAIN), and possible aggregation behavior were performed. The ligand similarity analysis, phylogenetic analysis of the receptors, and binding site analysis were also performed. The results revealed 17 bioactive and non-promiscuous compounds that have good physicochemical and pharmacokinetic properties. Six of the identified compounds bound to 15 or more receptors with a free energy value ≥ -7.0cal/mol.
Downloads
Article Details
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
How to Cite
References
Margret CR, Prabakaran M, Jaykar B, Venkateswarlu B, Palanisamy P. BRCA mutation: A review of breast cancer. J Drug Disc Ther. 2019; 9(2-s):617-624.
WHO. "Cancer Fact Sheet N 297". World Health Organization. February 2018. Retrieved 21 March 2018.
Global, regional and national life expectancy, all-cause mortality, and cause-specific mortality for 249 causes of death, 1980–2015: a systematic analysis for the Global Burden of Disease Study 2015. Lancet. 2016; 388(10053): 1459-1544.
Poetsch AR, Boulton SJ, Luscombe NM. Genomic landscape of oxidative DNA damage and repair reveals regioselective protection from mutagenesis. Genome Biol. 2018; 19:215.
Jefford C and Irminger-Finger I. Mechanisms of chromosome instability in cancers. Crit Rev Oncol Hematol. 2006; 59:1-14.
Howarth K, Blood K, Ng B, Beavis J, Chua Y, Cooke S. Chromosome translocations in breast cancer. Breast Cancer Res. 2008; 10(2):6.
Idowu MO and Powers CN. Lung cancer cytology: potential pitfalls and mimics - a review. Int J Clin Exp Pathol. 2010; 3(4):367-385.
Beatty LG and Whitney LG. Immune escape mechanisms as a guide for cancer immunotherapy. Clin Cancer Res.2015; 21(4):687-692.
Rowaiye AB, Asala T, Oli AN, Uzochukwu IC, Akpa A, Esimone CO. The Activating Receptors of Natural KillerCells and Their Inter-Switching Potentials. Curr Drug Targets. 2020; 21(16): 1733-1751.
Rigsby RE and Parker AB. Using the PyMOL application to reinforce visual understanding of protein structure. Biochem and Molecular Bio Education. 2016; 44(5):433-437.
Waterhouse A, Bertoni M, Bienert S, Studer G, Tauriello G, Gumienny R. SWISS-MODEL: homology modelling of protein structures and complexes. Nucl Acids Res. 2018; 46(1):296-303.
Williams CJ, Headd JJ, Moriarty NW, Prisant MG, Videau LL, Deis LN, Verma V, Keedy DA, Hintze BJ, Chen VB, Jain S, Lewis SM, Arendall III WB, Snoeyink J, Adams PD, Lovell SC, Richardson JS, Richardson DC. MolProbity: More and better reference data for improved all‐atom structure validation. Protein Sci. 2017; 27(1):293-315.
Ramachandran S, Kota P, Ding F, Dokholyan NV. Automated minimization of steric clashes in protein structures. Proteins. 2011; 79(1):261-270.
Dallakyan S and Olson AJ. Small-Molecule Library Screening by Docking with PyRx. Methods Mol Biol. 2015; 1263:243-250.
Kim S, Thiessen P, Bolton E, Chen J, Fu G, Gindulyte A, Han L, He J, He S, Shoemaker B, Wang J, Yu B, Zhang J, Bryant S. PubChem Substance and Compound databases. Nucl Acids Res. 2016; 44(D1):D1202-D1213.
Daina A, Michielin O, Zoete V. SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep. 2017; 7:42717.
Backman TW, Cao Y, Girke T. ChemMine tools: an online service for analyzing and clustering small molecules. NuclAcids Res. 2011; 39:W486-91.
Sievers F and Higgins DG. Clustal Omega for making accurate alignments of many protein sequences. Protein Sci.2018; 27(1):135-145.
Salentin S. PLIP: fully automated protein-ligand interaction profiler. Nucl Acids Res. 2015; 43(W1):W443-W447.
Kuriata A, Aleksandra M, Gierut T, Oleniecki MP, Ciemny A, Kolinski M, Kurcinski SK. CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures. Nucl Acids Res. 2018; 46(W1):W338-W343.
Xiang Z. Advances in homology protein structure modeling. Curr Prot Pept Sci. 2006; 7(3):217-227.
Ginalski K. Comparative modeling for protein structure prediction. Curr Opin Struct Biol. 2006; 16(2):172-177.
Das D, and Mukhopadhyay S. Studying backbone torsional dynamics of intrinsically disordered proteins using fluorescence depolarization kinetics. J Biosci. 2018; 43:455-462.
Chen B, Vincent W, Bryan AIII, Jeffrey JH, Daniel AK, Robert MI. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr. 2010; 66(1):12-21.
Subramani A and Floudas CA. Structure Prediction of Loops with Fixed and Flexible Stems. J Phys Chem B. 2012; 116(23):6670-6682.
Schneider M, Fu X, Keating AE. X‐ray vs. NMR structures as templates for computational protein design. Proteins: Struct Funct Bioinform. 2009; 77(1):97-110.
Kushwah YS and Shrivastava RK. Energy minimization of protein structure using homology modeling and Particle Swarm Optimization with Dynamic Inertia Weights. IOSR J Comput Eng. 2017; 19(6):24-31
Shivanika C, Deepak KS, Venkataraghavan R, Pawan T,Sumitha A, Brindha DP. Molecular docking, validation, dynamics simulations, and pharmacokinetic prediction of natural compounds against the SARS-CoV-2 main-protease. J Biomol Structure Dynam. 2020 (Sept 8): 1–27.
Morak-Młodawska B, Pluta K, Jele M. Evaluation of the Lipophilicity of New Anticancer 1,2,3-TriazoleDipyridothiazine Hybrids Using RP TLC and Different omputational Methods. Processes 2020; 8(7):8580.
Isa MA, Mustapha A, Qazi S, Raza K, Allamin IA, Ibrahim MM & Mohammed MM. In silico molecular docking and molecular dynamic simulation of potential inhibitors of 3Clike main proteinase (3CLpro) from severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) using selected African medicinal plants. Adv Trad Med. 2020 (Nov 19): 1–17.
Zhang MQ and Wilkinson B. Drug discovery beyond the 'rule-of-five'. Curr Opin Biotechnol. 2007; 18(6):478-88.
Ganesan A. The impact of natural products upon modern drug discovery. Curr Opin Chem Biol. 2008; 12(3):306- 317.
Paricharak S, Méndez-Lucio O, Ravindranath AC, Bender A, IJzerman AP, van Westen GJP (2018. Data-driven approaches used for compound library design, hit triage and bioactivity modeling in high-throughput screening. Briefings in Bioinformat. 2018; 19(2):277-285.
Hopkins AL. Pharmacological Space in the Practice of Medicinal Chemistry. (4th ed.). Pages 395-408.USA: Elsevier; 2015.
Zingoni A, Molfetta R, Fionda C, Soriani A, Paolini R, Marco Cippitelli, Cristina Cerboni and Angela Santoni. NKG2D and Its Ligands: ―One for All, All for One‖. FrontImmunol. 2018; 9: 476.
Vlieg HC, Huizinga EG, Janssen BJC. Structure and flexibility of the extracellular region of the PirB receptor. J Biol Chem. 2019; 294:4634-4643.
Schnell DJ. The TOC GTPase Receptors: Regulators of the Fidelity, Specificity and Substrate Profiles of the General Protein Import Machinery of Chloroplasts. Protein J. 2019; 38:343-350.
James SS and Michael JW. Practical application of ligand efficiency metrics in lead optimization. Bioorg Med Chem. 2018; 26(11):3006-3015.
Zhu T, Shuyi C, Pin-Chih S, Ram Patel, Darshan S, Heta BC. Hit Identification and Optimization in Virtual Screening: Practical Recommendations Based Upon a Critical Literature Analysis. J Med Chem. 2013; 56(17):6560-6572.
Kenny PW. The nature of ligand efficiency. J Cheminform. 2019; 11:8.
Von Korff M and Sander T. Molecular Complexity Calculated by Fractal Dimension. Sci Rep. 2019; 9:967.
Feldmann C, Miljković F, Yonchev D, and Bajorath J.Identifying Promiscuous Compounds with Activity against Different Target Classes. Molecules. 2019; 24(22):4185.
Dhillon B, Narendra KG, Rishabha M, Pramod KS. Poorly Water-Soluble Drugs: Change in Solubility for Improved Dissolution Characteristics - A Review. Glob J Pharmacol.2014; 8(1):26-35.
Szisz D and Antal L. Solubility prediction - ChemAxon's Solubility Predictor. [Online]. 2018. Available from: https://chemaxon.com/news/solubility-predictionchemaxons-solubility-predictor. Accessed on the 4th of April, 2020
Van-Breemen RB and Li Y. Caco-2 cell permeability assays to measure drug absorption. Expert Opin Drug Metab Toxicol. 2005; 1(2):175-185.
Basant N, Gupta S, Singh KP. Predicting human intestinal absorption of diverse chemicals using ensemble learning based QSAR modeling approaches. Comput Biol Chem. 2016; 61:178-196.
Faralli A, Shekarforoush E, Ajalloueian F, Mendes AC, Chronakis IS. In vitro permeability enhancement of curcumin across Caco-2 cells monolayers using electrospun xanthan-chitosan nanofibers. Carbohydr Polym. 2019; 15(206):38-47.
Waghray D and Zhang Q. Inhibit or Evade Multidrug Resistance P-glycoprotein in Cancer Treatment. J Med Chem. 2018; 61(12):5108-5121.
Han Y, Zhang J, Hu CQ, Zhang X, Ma B, Zhang P. In silico ADME and Toxicity Prediction of Ceftazidime and Its Impurities. Front Pharmacol. 2019; 10:434.
Lewis DF. Human cytochromes P450 associated with the phase 1 metabolism of drugs and other xenobiotics: a compilation of substrates and inhibitors of the CYP1, CYP2 and CYP3 families. Curr Med Chem. 2003; 10:1955-1972.
Stavropoulou E, Pircalabioru GG, Bezirtzoglou E. The Role of Cytochromes P450 in Infection. Front Immunol. 2018; 9:89.
Pires DEV, Blundell TL, Ascher DB. pkCSM: predicting small-molecule pharmacokinetic properties using graphbased signatures. Journal of Medicinal Chemistry. 2015; 58 (9): 4066–4072.
Hu J, Webster D, Cao J, Shao A. The safety of green tea and green tea extract consumption in adults – Results of a systematic review. Regulatory Toxicology and Pharmacology. 2018; 95:412-433.
Khan T, Shalini D, Rumana A, Saman R, Iqbal A, Seema J, Abdul RK. Molecular docking, PASS analysis, bioactivity score prediction, synthesis, characterization and biological activity evaluation of a functionalized 2-utanone
thiosemicarbazone ligand and its complexes. J Chem Biol.2017; 10(3):91-104.
Eaton BE, Gold L, Zchi DA. Let's get specific: the relationship between specificity and affinity. Chem Biol. 1995; 2(10):633-638.
Guo ZR. Drug promiscuity. Yao Xue Xue Bao. 2011; 46(4):361-369.
Tanford C. Chemical basis for antibody diversity and specificity. Accounts of Chem Res. 1968; 1(6):161-167.
Kubinyi H. Chemical Similarity and Biological Activities. J Braz Chem Soc. 2002; 13(6):717-726.
Che J, Wang Z, Sheng H, Huang F, Dong X, Hu Y, Xie X, Hu Y. Ligand-based pharmacophore model for the discovery of novel CXCR2 antagonists as anti-cancer metastatic agents. R Soc Open Sci. 2018; 5:180176.
Croce G, Gueudré T, Ruiz Cuevas MV, Keidel V, Figliuzzi M, Szurmant H, Weigt M. A multi-scale coevolutionary approach to predict interactions between protein domains. PLoS Comput Biol. 2019; 15(10):e1006891.
Wang Y, Wu H, Cai Y. A benchmark study of sequence alignment methods for protein clustering BMC Bioinformatics. 2018; 19(19):529.
Stauber DJ, Debler EW, Horton PA, Smith KA, Wilson IA. Crystal structure of the IL-2 signaling complex: paradigm for a heterotrimeric cytokine receptor. Proc Natl Acad Sci. 2006; 103(8):2788-2793.
Güldenhaupt J, Amaral M, Kötting C, JSchartner J, Musil D, Frech M, and Gerwert K. Ligand‐Induced Conformational Changes in HSP90 Monitored Time Resolved and Label Free—Towards a Conformational Activity Screening for Drug Discovery. Angew Chem Int Ed Engl. 2018; 57(31):9955-9960.
Mishra SK, Tripathi S, Shukla A, Oh SH, Kim HM. Andrographolide and analogues in cancer prevention (Elite Ed). Front Biosci. 2015; 7:255-266.
Puri A, Saxena R, Saxena RP, Saxena KC, Srivastava V, Tandon JS. Immunostimulant agents from Andrographis paniculata. J Nat Prod. 1993; 56(7):995-999.
Sheeja K and Kuttan G. Modulation of natural killer cell activity, antibody-dependent cellular cytotoxicity, and antibody-dependent complement-mediated cytotoxicity by andrographolide in normal and Ehrlich ascites carcinomabearing mice. Integr Cancer Ther. 2007; 6(1):66-73.
Sheeja K and Kuttan G. Andrographis paniculata downregulates proinflammatory cytokine production and augments cell mediated immune response in metastatic tumor-bearing mice. Asian Pac J Cancer Prev. 2010; 11(3):723-729.
Asami T and Nakagawa Y. Brief review of plant hormones and their utilization in agriculture. J Pest Sci. 2018; 43(3):154-158.
Koshioka MT and Nishijima HY. Endogenous gibberellins in the immature seeds of okra (Abelmoschus esculentus). J Plant Physiol. 1996:149(1–2):129-132.
Yu-xian Z, Davies PJ, Halinska A. Metabolism of Gibberellin A12 and A12-Aldehyde in Developing Seeds of Pisum sativum L. Plant Physiol. 1991; 97:26-33.
Scha¨fer P, Stefanie P1, Lars M, Doreen Z, Peter M, Chandler FW. Karl-Heinz K. Manipulation of plant innate immunity and gibberellin as factor of compatibility in the mutualistic association of barley roots with Piriformospora indica. The Plant J. 2009; 59:461-474.
Vidhyasekaran P. Plant Hormone Signaling Systems in Plant Innate Immunity. Part of the Signaling and Communication in Plants book series. SIGCOMM. 2014; 2:383-401.
Zhang Y, Hui Z, Jingbo C, Haixia Z, Xianghui Z, Hongbin Z, Chen Q. Antitumor and antiangiogenic effects of GA-13315, a gibberellin derivative. Investig New Drugs. 2012; 30(1):8-16.
Shen S and Tang J. Effects and mechanism of GA-13315 on the proliferation and apoptosis of KB cells in oral cancer. Oncol. Letters 2017; 14(2):1460-1463.
Mo J, Kang M, Ye JX, Chen JB, Zhang HB, Qing C. Gibberellin derivative GA-13315 sensitizes multidrugresistant cancer cells by antagonizing ABCB1 while agonizes ABCC1. Cancer Chemother Pharmacol. 2016; 78(1):51-61.
Chen J, Sun Z, Zhang Y, Zeng X, Qing C, Liu J, Li L, Zhang H. Synthesis of gibberellin derivatives with antitumor bioactivities. Bioorg Med Chem Lett. 2009; 19(18):5496-5499.
Murata T, Fushinobu S, Nakajima M, Asami O, Sassa T, Wakagi T, Yamaguchi SI. Crystal structure of the liganded anti-gibberellin A (4) antibody 4-B8(8)/E9 Fab fragment. Biochem Biophys Res Commun. 2002; 293(1):489-496.
Tringali C, Carmela S, Onofrio DL. Bioactive constituents of the bark of Parkia biglobosa. Fitoterapia. 2000; 71(2):118-125.
Yashi AY, Boris VN, Emilie C, Yakov IY. Determination of the Chemical Composition of Tea by Chromatographic Methods: A Review. J Food Res. 2015; 4(3): 56-88.
Khan N and Mukhtar H. Multitargeted Therapy of Cancer by Green Tea Polyphenols. Cancer Lett. 2008; 269(2):269-280.
Orentas RJ. Reading the tea leaves of tumor-mediated immunosuppression. Clin Cancer Res. 2013; 19(5):955-957.
So-Youn M, Mei Y, Sang BK, Sneha R, Seong-Ryuel K, Kamala V, Ho-Youn K, Laurie SD. Green Tea Epigallocatechin-3-Gallate Suppresses Autoimmune Arthritis Through Indoleamine-2,3-Dioxygenase Expressing Dendritic Cells and the Nuclear Factor, Erythroid 2-Like 2
Antioxidant Pathway. J Inflamm. 2015; 12:53.
Chen X, Li X, Zhai X, Zhi X, Cao L, Qin L, Su J. Shikimic Acid Inhibits Osteoclastogenesis in Vivo and in Vitro by Blocking RANK/TRAF6 Association and Suppressing NF-κB and MAPK Signaling Pathways. Cell Physiol Biochem.2018; 51:2858-2871.
Lima LGB, Montenegro J, de Abreu JP, Santos MCB, do Nascimento TP, Santos MD, Ferreira AG, Cameron LC, Ferreira MSL and Teodoro AJ. Metabolite Profiling by UPLC-MSE, NMR, and Antioxidant Properties of Amazonian Fruits: Mamey Apple (Mammea americana), Camapu (Physalis angulata), and Uxi (Endopleura uchi). Molecules 2020; 25:342.
Farrell N, Roberts JD, Hacker MP. Shikimic acid complexes of platinum. Preparation, reactivity, and antitumor activity of (R,R-1,2-diaminocyclohexane) bis(shikimate) platinum (II). Evidence for a novel rearrangement involving platinum-carbon bond formation. J
Inorg Biochem. 1991; 42(4):237-246.
Zhang Y, Liu A, Ye ZG, Lin J, Xu LZ, Yang SL. New approach to the total synthesis of (-)-zeylenone from shikimic acid. Chem Pharm Bull. 2006; 54:1459.
Sánchez-Abella L, Fernández S, Armesto N, Ferrero M, Gotor V. Novel and efficient syntheses of (-)-methyl 4-epishikimate and 4,5-epoxyquinic and -shikimic acid derivatives as key precursors to prepare new analogues. J Org Chem. 2006; 71(14):5396-5399.