Biopolym. Cell. 2019; 35(6): 448-466.
Identification and characterization of potential membrane-bound molecular drug targets of methicillin-resistant Staphylococcus aureus using in silico approaches
1Pernatii A. Yu., 1Volynets G. P., 1Protopopov M. V., 1, 2Prykhod’ko A. O., 1Sapelkin V. M., 1Pletnova L. V., 1, 2Matiushok V. I., 1Bdzhola V. G., 1Yarmoluk S. M.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03143
  2. LLC “Scientific and service firm “Otava”
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03143


Aim. The objective of this study was to identify the novel putative drug targets of methicil-lin-resistant S. aureus (MRSA) through subtractive proteome analysis. Methods. Identification of non-homologous proteins to the human proteome, search of MRSA essential genes and evaluation of drug target novelty were performed using protein BLAST server. Unique metabolic pathways identification was carried out using data and tools from KEGG (Kyoto Encyclopedia of Genes and Genomes). Prediction of sub-cellular proteins localization was performed using combination of tools PSORT v. 3.0.2, CELLO v. 2.5, iLoc-Gpos, and Pred-Lipo. Homology modeling was performed by web-servers SWISS-MODEL, Phyre2, I-TASSER, and program MODELLER. Results. Proteomes of six annotated methicillin-resistant strains, i.e., MRSA ATCC BAA-1680, H-EMRSA-15, LA MRSA ST398, MRSA 252, MRSA ST772, UTSW MRSA 55, have been taken to form the initial set. The proteome analysis of the MRSA strains in several consequent steps resulted in [the] identification of two molecular targets – diadenylate cyclase and D-alanyl-lipoteichoic acid biosynthesis (DltB) protein which meet the requirements of being essential, membrane-bound, non-homologous to human proteome, involved in unique metabolic pathways and new in terms of not having approved drugs. Using [the] homology modeling approach we have built three-dimensional structures of these proteins and predicted their ligand-binding sites. Conclusions. In this study using classical bioinformatics approaches we identified two molecular targets of MRSA – diadenylate cyclase and D-alanyl-lipoteichoic acid biosynthesis protein which can be used for further rational drug design in order to find novel therapeutic agents for the treatment of multidrug resistant staphylococcal infection.
Keywords: molecular drug targets, methicillin-resistant Staphylococcus aureus, MRSA, subtractive proteome analysis, homology modeling


[1] Jenkins A, An Diep B, Mai TT, Vo NH, Warrener P, Suzich J, Kendall Stover C, Sellman BR. Differential expression and roles of Staphylococcus aureus virulence determinants during colonization and disease. MBio 2015; 6(1): e02272-14.
[2] Holmes NE, Tong SYC, Davis JS, Hal SJV. Treatment of methicillin-resistant staphylococcus aureus: Vancomycin and beyond. Semin Respir Crit Care Med 2015; 36(1): 17-30.
[3] Kwon J, Mistry T, Ren J, Johnson ME, Mehboob S. A novel series of enoyl reductase inhibitors targeting the ESKAPE pathogens, Staphylococcus aureus and Acinetobacter baumannii. Bioorganic Med Chem 2018; 26(1): 65-76.
[4] Kronenberger T, Asse LR, Wrenger C, Trossini GHG, Honorio KM, Maltarollo VG. Studies of Staphylococcus aureus FabI inhibitors: Fragment-based approach based on holographic structure-activity relationship analyses. Future Med Chem 2017; 9(2): 135-51.
[5] Yu JY, Cheng HJ, Wu HR, Wu WS, Lu JW, Cheng TJ, Wu YT, Fang JM. Structure-based design of bacterial trans-glycosylase inhibitors incorporating biphenyl, amine linker and 2-alkoxy-3-phosphorylpropanoate moieties. Eur J Med Chem 2018; 150:729-41.
[6] Wu WS, Cheng WC, Cheng TJR, Wong CH. Affinity-Based Screen for Inhibitors of Bacterial Transglycosylase. J Am Chem Soc 2018; 140(8): 2752-5.
[7] Niu X, Gao Y, Yu Y, Yang Y, Wang G, Sun L, Wang H. Molecular Modelling reveals the inhibition mechanism and structure-activity relationship of curcumin and its analogues to Staphylococcal aureus Sortase A. J Biomol Struct Dyn 2019; 37(5): 1220-30.
[8] Chan AH, Yi SW, Weiner EM, Amer BR, Sue CK, Wereszczynski J, Dillen CA, Senese S, Torres JZ, McCammon JA, Miller LS, Jung ME, Clubb RT. NMR structure-based optimization of Staphylococcus aureus sortase A pyridazi-none inhibitors. Chem Biol Drug Des 2017; 90(3): 327-44.
[9] He W, Zhang Y, Bao J, Deng X, Batara J, Casey S, Guo Q, Jiang F, Fu L. Synthesis, biological evaluation and molecular docking analysis of 2-phenyl-benzofuran-3-carboxamide derivatives as potential inhibitors of Staphy-lococcus aureus Sortase A. Bioorganic Med Chem 2017; 25(4): 1341-51.
[10] Zhang B, Wang X, Wang L, Chen S, Shi D, Wang H. Molecular mechanism of the flavonoid natural product dryo-crassin ABBA against Staphylococcus aureus sortase A. Molecules 2016; 21(11): pii: E1428.
[11] Rentero Rebollo I, McCallin S, Bertoldo D, Entenza JM, Moreillon P, Heinis C. Development of Potent and Selective S aureus Sortase A Inhibitors Based on Peptide Macrocycles. ACS Med Chem Lett 2016; 7(6): 606-11.
[12] Maggio B, Raffa D, Raimondi MV, Cascioferro S, Plescia F, Schillaci D, Cusimano MG, Leonchiks A, Zhulenkovs D, Basile L, Daidone G. Discovery of a new class of sortase a transpeptidase inhibitors to tackle gram-positive pathogens: 2-(2-phenylhydrazinylidene)alkanoic acids and related derivatives. Molecules 2016; 21(2): 241.
[13] Gao C, Uzelac I, Gottfries J, Eriksson LA. Exploration of multiple Sortase A protein conformations in virtual screening. Sci Rep 2016; 6: 204-213.
[14] Ni S, Li B, Chen F, Wei H, Mao F, Liu Y, Xu Y, Qiu X, Li X, Liu W, Hu L, Ling D, Wang M, Zheng X, Zhu J, Lan L, Li J. Novel Staphyloxanthin Inhibitors with Improved Potency against Multidrug Resistant Staphylococcus au-reus. ACS Med Chem Lett 2018; 9(3): 233-7.
[15] Wei H, Mao F, Ni S, Chen F, Li B, Qiu X, Hu L, Wang M, Zheng X, Zhu J, Lan L, Li J. Discovery of novel piperonyl derivatives as diapophytoene desaturase inhibitors for the treatment of methicillin-, vancomycin- and line-zolid-resistant Staphylococcus aureus infections. Eur J Med Chem 2018; 145:235-51.
[16] Wang Y, Di H, Chen F, Xu Y, Xiao Q, Wang X, Wei H, Lu Y, Zhang L, Zhu J, Lan L, Li J. Discovery of Benzo-cycloalkane Derivatives Efficiently Blocking Bacterial Virulence for the Treatment of Methicillin-Resistant S au-reus (MRSA) Infections by Targeting Diapophytoene Desaturase (CrtN). J Med Chem 2016; 59(10): 4831-48.
[17] Chen F, Di H, Wang Y, Cao Q, Xu B, Zhang X, Yang N, Liu G, Yang CG, Xu Y, Jiang H, Lian F, Zhang N, Li J, Lan L. Small-molecule targeting of a diapophytoene desaturase inhibits S aureus virulence. Nat Chem Biol 2016; 12(3): 174-9.
[18] Bielenica A, Drzewiecka-Antonik A, Rejmak P, Stefańska J, Koliński M, Kmiecik S, Lesyng B, Włodarczyk M, Pietrzyk P, Struga M. Synthesis, structural and antimicrobial studies of type II topoisomerase-targeted copper(II) complexes of 1,3-disubstituted thiourea ligands. J Inorg Biochem 2018; 182:61-70.
[19] Alagumuthu M, Arumugam S. Molecular docking, discovery, synthesis, and pharmacological properties of new 6-substituted-2-(3-phenoxyphenyl)-4-phenyl quinoline derivatives; an approach to developing potent DNA gyrase inhibitors/antibacterial agents. Bioorganic Med Chem 2017; 25(4): 1448-55.
[20] Tan CM, Gill CJ, Wu J, Toussaint N, Yin J, Tsuchiya T, Garlisi CG, Kaelin D, Meinke PT, Miesel L, Olsen DB, Lagrutta A, Fukuda H, Kishii R, Takei M, Oohata K, Takeuchi T, Shibue T, Takano H, Nishimura A, Fukuda Y, Singh SB. In vitro and in vivo characterization of the novel oxabicyclooctane-linked bacterial topoisomerase inhibitor AM-8722, a selective, potent inhibitor of bacterial DNA gyrase. Antimicrob Agents Chemother 2016; 60(8): 4830-9.
[21] Zidar N, Tomašič T, Macut H, Sirc A, Brvar M, Montalvão S, Tammela P, Ilaš J, Kikelj D. New N-phenyl-4,5-dibromopyrrolamides and N-Phenylindolamides as ATPase inhibitors of DNA gyrase. Eur J Med Chem 2016; 117:197-211.
[22] Durcik M, Tammela P, Barančoková M, Tomašič T, Ilaš J, Kikelj D, Zidar N. Synthesis and Evaluation of N-Phenylpyrrolamides as DNA Gyrase B Inhibitors. ChemMedChem 2018; 13(2): 186-98.
[23] Mitton-Fry MJ, Brickner SJ, Hamel JC, Barham R, Brennan L, Casavant JM, Ding X, Finegan S, Hardink J, Hoang T, Huband MD, Maloney M, Marfat A, McCurdy SP, McLeod D, Subramanyam C, Plotkin M, Reilly U, Schafer J, Stone GG, Uccello DP, Wisialowski T, Yoon K, Zaniewski R, Zook C. Novel 3-fluoro-6-methoxyquinoline derivatives as inhibitors of bacterial DNA gyrase and topoisomerase IV. Bioorganic Med Chem Lett 2017; 27(15): 3353-8.
[24] Surivet JP, Zumbrunn C, Bruyère T, Bur D, Kohl C, Locher HH, Seiler P, Ertel EA, Hess P, Enderlin-Paput M, Enderlin-Paput S, Gauvin JC, Mirre A, Hubschwerlen C, Ritz D, Rueedi G. Synthesis and Characterization of Te-trahydropyran-Based Bacterial Topoisomerase Inhibitors with Antibacterial Activity against Gram-Negative Bacteria. J Med Chem 2017; 60(9): 3776-94.
[25] Jakopin Ž, Ilaš J, Barančoková M, Brvar M, Tammela P, Sollner Dolenc M, Tomašič T, Kikelj D. Discovery of substituted oxadiazoles as a novel scaffold for DNA gyrase inhibitors. Eur J Med Chem 2017; 130:171-84.
[26] Gjorgjieva M, Tomašič T, Barančokova M, Katsamakas S, Ilaš J, Tammela P, Mašič LP, Kikelj D. Discovery of Benzothiazole Scaffold-Based DNA Gyrase B Inhibitors. J Med Chem 2016; 59(19): 8941-54.
[27] Savage VJ, Charrier C, Salisbury AM, Moyo E, Forward H, Chaffer-Malam N, Metzger R, Huxley A, Kirk R, Uosis-Martin M, Noonan G, Mohmed S, Best SA, Ratcliffe AJ, Stokes NR. Biological profiling of novel tricyclic inhibitors of bacterial DNA gyrase and topoisomerase IV. J Antimicrob Chemother 2016; 71(7): 1905-13.
[28] Ballu S, Itteboina R, Sivan SK, Manga V. Structural insights of Staphylococcus aureus FtsZ inhibitors through molecular docking, 3D-QSAR and molecular dynamics simulations. J Recept Signal Transduct 2018; 38(1): 61-70.
[29] Bi F, Guo L, Wang Y, Venter H, Semple SJ, Liu F, Ma S. Design, synthesis and biological activity evaluation of novel 2,6-difluorobenzamide derivatives through FtsZ inhibition. Bioorganic Med Chem Lett 2017; 27(4): 958-62.
[30] Qiang S, Wang C, Venter H, Li X, Wang Y, Guo L, Ma R, Ma S. Synthesis and Biological Evaluation of Novel FtsZ-targeted 3-arylalkoxy-2,6-difluorobenzamides as Potential Antimicrobial Agents. Chem Biol Drug Des 2016; 87(2): 257-64.
[31] Hrast M, Jukič M, Patin D, Tod J, Dowson CG, Roper DI, Barreteau H, Gobec S. In silico identification, synthesis and biological evaluation of novel tetrazole inhibitors of MurB. Chem Biol Drug Des 2018; 91(6): 1101-12.
[32] Vickery CR, Wood BMK, Morris HG, Losick R, Walker S. Reconstitution of Staphylococcus aureus Lipoteichoic Acid Synthase Activity Identifies Congo Red as a Selective Inhibitor. J Am Chem Soc 2018; 140(3): 876-9.
[33] Paparella AS, Lee KJ, Hayes AJ, Feng J, Feng Z, Cini D, Deshmukh S, Booker GW, Wilce MCJ, Polyak SW, Abell AD. Halogenation of Biotin Protein Ligase Inhibitors Improves Whole Cell Activity against Staphylococcus aureus. ACS Infect Dis 2018; 4(2): 175-84.
[34] Feng J, Paparella AS, Booker GW, Polyak SW, Abell AD. Biotin protein ligase is a target for new antibacterials. Antibiotics 2016; 5(3): pii: E26
[35] Merzoug A, Chikhi A, Bensegueni A, Boucherit H, Okay S. Virtual Screening Approach of Bacterial Peptide De-formylase Inhibitors Results in New Antibiotics. Mol Inform 2018; 37(3).
[36] Schaenzer AJ, Wlodarchak N, Drewry DH, Zuercher WJ, Rose WE, Striker R, Sauer JD. A screen for kinase inhi-bitors identifies antimicrobial imidazopyridine aminofurazans as specific inhibitors of the Listeria monocytogenes PASTA kinase PrkA. J Biol Chem 2017; 292(41): 17037-45.
[37] Wang B, Huang W, Zhou J, Tang X, Chen Y, Peng C, Han B. Drug design based on pentaerythritol tetranitrate reductase: Synthesis and antibacterial activity of Pogostone derivatives. Org Biomol Chem 2017; 15(31): 6548-56.
[38] Gao J, Qiu S, Liang L, Hao Z, Zhou Q, Wang F, Mou J, Lin Q. Design, Synthesis, and Biological Evaluation of Vanillin Hydroxamic Acid Derivatives as Novel Peptide Deformylase Inhibitors. Curr Comput Aided Drug Des 2018; 14(1): 95-101.
[39] Singh A, Srivastava R, Singh RK. Design, Synthesis, and Antibacterial Activities of Novel Heterocyclic Arylsul-phonamide Derivatives. Interdiscip Sci Comput Life Sci 2018; 10(4): 748-61.
[40] Felicetti T, Cannalire R, Burali MS, Massari S, Manfroni G, Barreca ML, Tabarrini O, Schindler BD, Sabatini S, Kaatz GW, Cecchetti V. Searching for Novel Inhibitors of the S aureus NorA Efflux Pump: Synthesis and Biolog-ical Evaluation of the 3-Phenyl-1,4-benzothiazine Analogues. ChemMedChem 2017; 12(16): 1293-302.
[41] Astolfi A, Felicetti T, Iraci N, Manfroni G, Massari S, Pietrella D, Tabarrini O, Kaatz GW, Barreca ML, Sabatini S, Cecchetti V. Pharmacophore-Based Repositioning of Approved Drugs as Novel Staphylococcus aureus NorA Efflux Pump Inhibitors. J Med Chem 2017; 60(4): 1598-604.
[42] Buonerba F, Lepri S, Goracci L, Schindler BD, Seo SM, Kaatz GW, Cruciani G. Improved Potency of In-dole-Based NorA Efflux Pump Inhibitors: From Serendipity toward Rational Design and Development. J Med Chem 2017; 60(1): 517-23.
[43] Bhaskar BV, Chandra Babu TM, Reddy NV, Rajendra W. Homology modeling, molecular dynamics, and virtual screening of nora efflux pump inhibitors of Staphylococcus aureus. Drug Des Devel Ther 2016; 10:3237-52.
[44] Costa LM, de Macedo E V., Oliveira FAA, Ferreira JHL, Gutierrez SJC, Peláez WJ, Lima FCA, de Siqueira Júnior JP, Coutinho HDM, Kaatz GW, de Freitas RM, Barreto HM. Inhibition of the NorA efflux pump of Sta-phylococcus aureus by synthetic riparins. J Appl Microbiol 2016; 121(5): 1312-22.
[45] Wani NA, Singh S, Farooq S, Shankar S, Koul S, Khan IA, Rai R. Amino acid amides of piperic acid (PA) and 4-ethylpiperic acid (EPA) as NorA efflux pump inhibitors of Staphylococcus aureus. Bioorganic Med Chem Lett 2016; 26(17): 4174-8.
[46] Liger F, Bouhours P, Ganem-Elbaz C, Jolivalt C, Pellet-Rostaing S, Popowycz F, Paris JM, Lemaire M. C2 Ary-lated Benzo[b]thiophene Derivatives as Staphylococcus aureus NorA Efflux Pump Inhibitors. ChemMedChem 2016; 11(3): 320-30.
[47] Gupta A, Mishra S, Singh S, Mishra S. Prevention of IcaA regulated poly N-acetyl glucosamine formation in Staphylococcus aureus biofilm through new-drug like inhibitors: In silico approach and MD simulation study. Microb Pathog 2017; 110:659-69.
[48] El-Gazzar YI, Georgey HH, El-Messery SM, Ewida HA, Hassan GS, Raafat MM, Ewida MA, El-Subbagh HI. Synthesis, biological evaluation and molecular modeling study of new (1,2,4-triazole or 1,3,4-thiadiazole)-methylthio-derivatives of quinazolin-4(3H)-one as DHFR inhibitors. Bioorg Chem 2017; 72: 282-92.
[49] Elbaramawi SS, Ibrahim SM, Lashine ESM, El-Sadek ME, Mantzourani E, Simons C. Exploring the binding sites of Staphylococcus aureus phenylalanine tRNA synthetase: A homology model approach. J Mol Graph Model 2017; 73: 36-47.
[50] Choi SR, Frandsen J, Narayanasamy P. Novel long-chain compounds with both immunomodulatory and MenA inhibitory activities against Staphylococcus aureus and its biofilm. Sci Rep 2017; 7: 40077.
[51] Cui P, Li X, Zhu M, Wang B, Liu J, Chen H. Design, synthesis and antibacterial activities of thiouracil derivatives containing acyl thiourea as SecA inhibitors. Bioorganic Med Chem Lett 2017; 27(10): 2234-7 .52. Feng J, Paparella AS, Tieu W, Heim D, Clark S, Hayes A, Booker GW, Polyak SW, Abell AD. New Series of BPL Inhibitors To Probe the Ribose-Binding Pocket of Staphylococcus aureus Biotin Protein Ligase. ACS Med Chem Lett 2016; 7(12): 1068-72.
[53] Swarupa V, Chaudhury A, Krishna Sarma PVG. Effect of 4-methoxy 1-methyl 2-oxopyridine 3-carbamide on Staphylococcus aureus by inhibiting UDP-MurNAc-pentapeptide, peptidyl deformylase and uridine monophos-phate kinase. J Appl Microbiol 2017; 122(3): 663-75.
[54] North RA, Watson AJA, Pearce FG, Muscroft-Taylor AC, Friemann R, Fairbanks AJ, Dobson RCJ. Structure and inhibition of N-acetylneuraminate lyase from methicillin-resistant Staphylococcus aureus. FEBS Lett 2016; 590(23): 4414-28.
[55] Marimuthu P, Singaravelu K, Namasivayam V. Probing the binding mechanism of mercaptoguanine derivatives as inhibitors of HPPK by docking and molecular dynamics simulations. J Biomol Struct Dyn 2017; 35(16): 3507-21.
[56] Dennis ML, Pitcher NP, Lee MD, Debono AJ, Wang ZC, Harjani JR, Rahmani R, Cleary B, Peat TS, Baell JB, Swarbrick JD. Structural Basis for the Selective Binding of Inhibitors to 6-Hydroxymethyl-7,8-dihydropterin Py-rophosphokinase from Staphylococcus aureus and Escherichia coli. J Med Chem 2016; 59(11): 5248-63.
[57] Ye F, Li J, Yang CG. The development of small-molecule modulators for ClpP protease activity. Mol Biosyst 2017; 13(1): 23-31.
[58] Kakarla P, Floyd J, Mukherjee MM, Devireddy AR, Inupakutika MA, Ranweera I, Kc R, Shrestha U, Cheeti UR, Willmon TM, Adams J, Bruns M, Gunda SK, Varela MF. Inhibition of the multidrug efflux pump LmrS from Staphylococcus aureus by cumin spice Cuminum cyminum. Arch Microbiol 2017; 199(3): 465-74.
[59] Herman-Bausier P, Valotteau C, Pietrocola G, Rindi S, Alsteens D, Foster TJ, Speziale P, Dufrêne YF. Mechani-cal strength and inhibition of the Staphylococcus aureus collagen-binding protein Cna. MBio. 2016; 7(5): pii: e01529-16.
[60] Hughes SJ, Barnard L, Mottaghi K, Tempel W, Antoshchenko T, Hong BS, Allali-Hassani A, Smil D, Vedadi M, Strauss E, Park HW. Discovery of potent pantothenamide inhibitors of staphylococcus Aureus Pantothenate Ki-nase through a minimal SAR Study: Inhibition Is Due to Trapping of the Product. ACS Infect Dis. 2016; 2(9): 627-41.
[61] Wang Y, Desai J, Zhang Y, Malwal SR, Shin CJ, Feng X, Sun H, Liu G, Guo RT, Oldfield E. Bacterial Cell Growth Inhibitors Targeting Undecaprenyl Diphosphate Synthase and Undecaprenyl Diphosphate Phosphatase. ChemMedChem. 2016; 11(20): 2311-9.
[62] Inokoshi J, Nakamura Y, Komada S, Komatsu K, Umeyama H, Tomoda H. Inhibition of bacterial undecaprenyl pyrophosphate synthase by small fungal molecules. J Antibiot (Tokyo). 2016; 69(11): 798-805.
[63] Concha N, Huang J, Bai X, Benowitz A, Brady P, Grady LC, Kryn LH, Holmes D, Ingraham K, Jin Q, Pothier Kaushansky L, McCloskey L, Messer JA, O'Keefe H, Patel A, Satz AL, Sinnamon RH, Schneck J, Skinner SR, Summerfield J, Taylor A, Taylor JD, Evindar G, Stavenger RA. Discovery and Characterization of a Class of Py-razole Inhibitors of Bacterial Undecaprenyl Pyrophosphate Synthase. J Med Chem. 2016; 59(15): 7299-304.
[64] Zaveri K, Kiranmayi P. Screening of Potential Lead Molecule as Novel MurE Inhibitor: Virtual Screening, Mo-lecular Dynamics and In Vitro Studies. Curr Comput Aided-Drug Des. 2016; 13(1): 8-21.
[65] Morvan C, Halpern D, Kénanian G, Hays C, Anba-Mondoloni J, Brinster S, Kennedy S, Trieu-Cuot P, Poyart C, Lamberet G, Gloux K, Gruss A. Environmental fatty acids enable emergence of infectious Staphylococcus aureus resistant to FASII-targeted antimicrobials. Nat Commun. 2016; 7: 12944.
[66] Labrière C, Gong H, Finlay BB, Reiner NE, Young RN. Further investigation of inhibitors of MRSA pyruvate kinase: Towards the conception of novel antimicrobial agents. Eur J Med Chem. 2017; 12: 51-13.
[67] El-Sayed MT, Zoraghi R, Reiner N, Suzen S, Ohlsen K, Lalk M, Altanlar N, Hilgeroth A. Novel inhibitors of the methicillin-resistant Staphylococcus aureus (MRSA)-pyruvate kinase. J Enzyme Inhib Med Chem. 2016; 31(6): 1666-71.
[68] Holden JK, Lewis MC, Cinelli MA, Abdullatif Z, Pensa A V., Silverman RB, Poulos TL. Targeting Bacterial Nitric Oxide Synthase with Aminoquinoline-Based Inhibitors. Biochemistry. 2016; 55(39): 5587-94.
[69] Zheng W, Cai X, Xie M, Liang Y, Wang T, Li Z. Structure-Based Identification of a Potent Inhibitor Targeting Stp1-Mediated Virulence Regulation in Staphylococcus aureus. Cell Chem Biol. 2016; 23(8): 1002-13.
[70] Skupińska M, Stȩpniak P, Łȩtowska I, Rychlewski L, Barciszewska M, Barciszewski J, Giel-Pietraszuk M. Natural compounds as inhibitors of Tyrosyl-tRNA synthetase. Microb Drug Resist. 2017; 23(3): 308-20.
[71] Desai J, Liu YL, Wei H, Liu W, Ko TP, Guo RT, Oldfield E. Structure, Function, and Inhibition of Staphylococcus aureus Heptaprenyl Diphosphate Synthase. ChemMedChem. 2016; 1915-23.
[72] Bommineni GR, Kapilashrami K, Cummings JE, Lu Y, Knudson SE, Gu C, Walker SG, Slayden RA, Tonge PJ. Thiolactomycin-Based Inhibitors of Bacterial β-Ketoacyl-ACP Synthases with in Vivo Activity. J Med Chem. 2016; 59(11): 5377-90.
[73] Czerwonka D, Domagalska J, Pyta K, Kubicka MM, Pecyna P, Gajecka M, Przybylski P. Structure-activity rela-tionship studies of new rifamycins containing l-amino acid esters as inhibitors of bacterial RNA polymerases. Eur J Med Chem. 2016; 116: 216-21.
[74] Hou Y, Mayhood T, Sheth P, Tan CM, Labroli M, Su J, Wyss DF, Roemer T, McCoy MA. NMR Binding and Functional Assays for Detecting Inhibitors of S aureus MnaA. J Biomol Screen. 2016; 21(6): 579-89.
[75] Joung DK, Lee YS, Han SH, Lee SW, Cha SW, Mun SH, Kong R, Kang OH, Song HJ, Shin DW, Kwon DY. Poten-tiating activity of luteolin on membrane permeabilizing agent and ATPase inhibitor against methicillin-resistant Staphylococcus aureus. Asian Pac J Trop Med. 2016; 9(1): 19-22.
[76] Addo JK, Skaff DA, Miziorko HM. Active site binding modes of inhibitors of Staphylococcus aureus mevalonate diphosphate decarboxylase from docking and molecular dynamics simulations. J Mol Model. 2016; 22(1): 1-18.
[77] Mesleh MF, Rajaratnam P, Conrad M, Chandrasekaran V, Liu CM, Pandya BA, Hwang YS, Rye PT, Muldoon C, Becker B, Zuegg J, Meutermans W, Moy TI. Targeting Bacterial Cell Wall Peptidoglycan Synthesis by Inhibition of Glycosyltransferase Activity. Chem Biol Drug Des. 2016; 87(2): 190-9.
[78] Vuong C, Yeh AJ, Cheung GYC, Otto M. Investigational drugs to treat methicillin-resistant Staphylococcus au-reus. Expert Opin Investig Drugs. 2016; 25(1): 73-93.
[79] Yadav PK, Singh G, Singh S, Gautam B, Saad EI. Potential therapeutic drug target identification in Community Acquired-Methicillin Resistant Staphylococcus aureus (CA-MRSA) using computational analysis. Bioinformation. 2012; 8(14): 664-72.
[80] Hossain M, Chowdhury DUS, Farhana J, Akbar MT, Chakraborty A, Islam S, Mannan A. Identification of poten-tial targets in Staphylococcus aureus N315 using computer aided protein data analysis. Bioinformation. 2013; 9(4): 187-92.
[81] Uddin R, Saeed K. Identification and characterization of potential drug targets by subtractive genome analyses of methicillin resistant Staphylococcus aureus. Comput Biol Chem. 2014; 48: 55-63.
[82] Uddin R, Saeed K, Khan W, Azam SS, Wadood A. Metabolic pathway analysis approach: Identification of novel therapeutic target against methicillin resistant Staphylococcus aureus. Gene. 2015; 556(2): 213-26.
[83] Hasan MA, Khan MA, Sharmin T, Hasan Mazumder MH, Chowdhury AS. Identification of putative drug targets in Vancomycin-resistant Staphylococcus aureus (VRSA) using computer aided protein data analysis. Gene 2016; 575(1): 132-43.84. Zhang R. DEG: a database of essential genes. Nucleic Acids Re.s 2004; 32(90001): 271D - 272D.
[85] Luo H, Lin Y, Gao F, Zhang CT, Zhang R. DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements. Nucleic Acids Res. 2014; 42(D1): 574-80.
[86] Kanehisa M, Goto S. Yeast Biochemical Pathways KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000; 28(1): 27-30.
[87] Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K. KEGG: New perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res. 2017; 45(D1): D353-61.
[88] Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. KAAS: An automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 2007; 35(SUPPL.2): 182-5.
[89] Wishart DS, Feunang YD, Guo AC, Lo EJ, Marcu A, Grant JR, Sajed T, Johnson D, Li C, Sayeeda Z, Assempour N, Iynkkaran I, Liu Y, MacIejewski A, Gale N, Wilson A, Chin L, Cummings R, Le Di, Pon A, Knox C, Wilson M. DrugBank 50: A major update to the DrugBank database for 2018. Nucleic Acids Res. 2018; 46(D1):D1074-82.
[90] Gardy JL, Brinkman FSL. Methods for predicting bacterial protein subcellular localization. Nat Rev Microbiol. 2006; 4(10):741-51.
[91] Yu CS, Chen YC, Hwang JK. Prediction of protein subcellular localization. Proteins. 2006; 64(3):643-651.
[92] Wu Z-C, Xiao X, Chou K-C. iLoc-Gpos: A Multi-Layer Classifier for Predicting the Subcellular Localization of Singleplex and Multiplex Gram-Positive Bacterial Proteins. Protein Pept Lett. 2012; 19(1):4-14.
[93] Bagos PG, Tsirigos KD, Liakopoulos TD, Hamodrakas SJ. Prediction of lipoprotein signal peptides in Gram-positive bacteria with a Hidden Markov Model. J Proteome Res. 2008; 7(12):5082-93.
[94] Swiss-Model web-server Accessed 1 November 2019.
[95] Waterhouse A, Bertoni M, Bienert S, Studer G, Tauriello G, Gumienny R, Heer FT, De Beer TAP, Rempfer C, Bordoli L, Lepore R, Schwede T. SWISS-MODEL: Homology modelling of protein structures and complexes. Nucleic Acids Res. 2018; 46(W1):W296-303.
[96] Guex N, Peitsch MC, Schwede T. Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: A historical perspective. Electrophoresis. 2009; 30: S162-S173.
[97] Bienert S, Waterhouse A, de Beer TAP, Tauriello G, Studer G, Bordoli L, Schwede T. The SWISS-MODEL Re-pository - new features and functionality. Nucleic Acids Res. 2017; 45: D313-D319.
[98] Benkert P, Biasini M, Schwede T. Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics. 2011; 27: 343-50.
[99] Bertoni M, Kiefer F, Biasini M, Bordoli L, Schwede T. Modeling protein quaternary structure of homo- and hete-ro-oligomers beyond binary interactions by homology. Sci Rep. 2017; 7: 10480.
[100] Phyre2 web-server Accessed 1 November 2019.
[101] Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJ. The Phyre2 web portal for protein modeling, predic-tion and analysis. Nat Protoc. 2015; 10(6): 845-58.
[102] I-TASSER web server Accessed 1 November 2019.
[103] Roy A, Kucukural A, Zhang Y. I-TASSER: a unified platform for automated protein structure and function pre-diction. Nat Protoc. 2010; 5:725-38.
[104] Yang J, Yan R, Roy A, Xu D, Poisson J, Zhang Y. The I-TASSER Suite: protein structure and function prediction. Nat Methods. 2015; 12: 7-8.
[105] Yang J, Zhang Y. I-TASSER server: new development for protein structure and function predictions. Nucleic Acids Res. 2015; 43: W174-W181.
[106] Webb B, Sali A. Comparative protein structure modeling using MODELLER. Curr Protoc Bioinformatics. 2016; 56: 5.6.1-5.6.37.
[107] Marti-Renom MA, Stuart A, Fiser A, Sanchez R, Melo F, Sali A. Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct. 2000; 29:291-325.
[108] Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol. 1993; 234: 779-815.
[109] Fiser A, Do RK, Sali A. Modeling of loops in protein structures. Protein Sci. 2000; 9: 1753-73.
[110] Hess B, Kutzner C, van der Spoel D, Lindahl E. GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput. 2008; 4: 435-47.
[111] Van der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJC. GROMACS: Fast, Flexible and Free. J Comp Chem. 2005; 26:1701-19.
[112] Berendsen HJC, van der Spoel D, van Drunen R. GROMACS: A message-passing parallel molecular dynamics implementation. Comp Phys Comm. 1995; 91: 43-56.
[113] Chen VB, Arendall WB, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Rich-ardson DC. MolProbity: All-atom structure validation for macromolecular crystallography. Acta Crystallogr Sect D Biol Crystallogr. 2010; 66(1):12-21.
[114] Konc J, Janežič D. ProBiS tools (algorithm, database, and web servers) for predicting and modeling of biologi-cally interesting proteins. Prog Biophys Mol Biol. 2017; 128: 24-32.
[115] Daum LT, Bumah VV, Masson-Meyers DS, Khubbar M, Rodriguez JD, Fischer GW, Enwemeka CS, Gradus S, Bhattacharyya S. Whole-genome sequence for methicillin-resistant Staphylococcus aureus strain ATCC BAA-1680. Genome Announc. 2016; 3(2): e00011-15.
[116] Sabirova JS, Xavier BB, Hernalsteens JP, De Greve H, Ieven M, Goossens H, Malhotra-Kumar S. Complete genome sequences of two prolific biofilm-forming Staphylococcus aureus isolates belonging to USA300 and EMRSA-15 clonal lineages. Genome Announc. 2014; 2(3):e00610-14.
[117] Golding GR, Bryden L, Levett PN, Mcdonald RR, Wong A, Graham MR, Tyler S, van Domselaar G, Mabon P, Kent H, Butaye P, Smith TC, Kadlec K, Schwarz S, Weese SJ, Mulvey MR. Whole-genome sequence of lives-tock-associated ST398 methicillin-resistant Staphylococcus aureus isolated from humans in Canada. J Bacterio.l 2012; 194(23):6627-8.
[118] Holden MTG, Feil EJ, Lindsay JA, Peacock SJ, Day NPJ, Enright MC, Foster TJ, Moore CE, Hurst L, Atkin R, Barron A, Bason N, Bentley SD, Chillingworth C, Chillingworth T, Churcher C, Clark L, Corton C, Cronin A, Doggett J, Dowd L, Feltwell T, Hance Z, Harris B, Hauser H, Holroyd S, Jagels K, James KD, Lennard N, Line A, Mayes R, Moule S, Mungall K, Ormond D, Quail MA, Rabbinowitsch E, Rutherford K, Sanders M, Sharp S, Simmonds M, Stevens K, Whitehead S, Barrell BG, Spratt BG, Parkhill J. Complete genomes of two clinical Sta-phylococcus aureus strains: Evidence for the evolution of virulence and drug resistance. Proc Natl Acad Sci U S A. 2004; 101(26): 9786-91.
[119] Steinig EJ, Andersson P, Harris SR, Sarovich DS, Manoharan A, Coupland P, Holden MTG, Parkhill J, Bentley SD, Robinson DA, Tong SYC. Single-molecule sequencing reveals the molecular basis of multidrug-resistance in ST772 methicillin-resistant Staphylococcus aureus. BMC Genomics. 2015; 16(1):388.
[120] Gaviria-Agudelo C, Aroh C, Tareen N, Wakeland EK, Kim M, Copley LA. Genomic heterogeneity of Methicillin resistant Staphylococcus aureus associated with variation in severity of illness among children with acute hema-togenous osteomyelitis. PLoS One. 2015; 10(6):e0130415.
[121] Hediger MA, Turk E, Wright EM. Homology of the human intestinal Na+/glucose and Escherichia coli Na+/proline cotransporters. Proc Natl Acad Sci U S A. 1989; 86(15):5748-52.
[122] Swango KL, Hymes J, Brown P, Wolf B. Amino acid homologies between human biotinidase and bacterial ali-phatic amidases: Putative identification of the active site of biotinidase. Mol Genet Metab. 2000; 69(2)111-115.
[123] Chen IT, Dixit A, Rhoads DD, Roufa DJ. Homologous ribosomal proteins in bacteria, yeast, and humans. Proc Natl Acad Sci U S A. 1986; 83(18):6907-11.
[124] Willers J, Lucchese A, Kanduc D, Ferrone S. Molecular mimicry of phage displayed peptides mimicking GD3 ganglioside. Peptides. 1999; 20(9):1021-6.
[125] Natale C, Giannini T, Lucchese A, Kanduc D. Computer-assisted analysis of molecular mimicry between human papillomavirus 16 E7 oncoprotein and human protein sequences. Immunol Cell Biol. 2000; 78(6):580-5.
[126] Opoku-Temeng C, Sintim HO. Inhibition of cyclic diadenylate cyclase, DisA, by polyphenols. Sci Rep. 2016; 6:25445.
[127] Opoku-Temeng C, Sintim HO. Potent inhibition of cyclic diadenylate monophosphate cyclase by the antiparasitic drug, suramin. Chem Commun. 2016; 52(19): 3754-7.
[128] Pasquina L, Santa Maria JP, McKay Wood B, Moussa SH, Matano LM, Santiago M, Martin SES, Lee W, Mere-dith TC, Walker S. A synthetic lethal approach for compound and target identification in Staphylococcus aureus. Nat Chem Biol. 2016; 12(1): 40-5.
[129] Rosenberg J, Dickmanns A, Neumann P, Gunka K, Arens J, Kaever V, Stülke J, Ficner R, Commichau FM. Structural and biochemical analysis of the essential diadenylate cyclase CdaA from Listeria monocytogenes. J Biol Chem. 2015; 290(10): 6596-606.