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Computational Antibiotics Book Andrew V DeLong, Jared C Harris, Brittany S Larcart, Chandler B Massey, Chelsie D Northcutt, Somuayiro N Nwokike, Oscar A Otieno, Harsh M Patel, Mehulkumar P Patel, Pratik Pravin Patel, Eugene I Rowell, Brandon M Rush, Marc-Edwin G Saint-Louis, Amy M Vardeman, Felicia N Woods, Giso Abadi, Thomas J. Manning Computational Antibiotics Valdosta State University is located in South Georgia. Computational Antibiotics Index • Computational Details and Website Access (p. 8) • Acknowledgements (p. 9) • Dedications (p. 11) • Antibiotic Historical Introduction (p. 13) Introduction to Antibiotic groups • Penicillin’s (p. 21) • Carbapenems (p. 22) • Oxazolidines (p. 23) • Rifamycin (p. 24) • Lincosamides (p. 25) • Quinolones (p. 26) • Polypeptides antibiotics (p. 27) • Glycopeptide Antibiotics (p. 28) • Sulfonamides (p. 29) • Lipoglycopeptides (p. 30) • First Generation Cephalosporins (p. 31) • Cephalosporin Third Generation (p. 32) • Fourth-Generation Cephalosporins (p. 33) • Fifth Generation Cephalosporin’s (p. 34) • Tetracycline antibiotics (p. 35) Computational Antibiotics Antibiotics Covered (in alphabetical order) Amikacin (p. 36) Cefempidone (p. 98) Ceftizoxime (p. 159) Amoxicillin (p. 38) Cefepime (p. 100) Ceftobiprole (p. 161) Ampicillin (p. 40) Cefetamet (p. 102) Ceftoxide (p. 163) Arsphenamine (p. 42) Cefetrizole (p. 104) Ceftriaxone (p. 165) Azithromycin (p.44) Cefivitril (p. 106) Cefuracetime (p. 167) Aziocillin (p. 46) Cefixime (p. 108) Cefuroxime (p. 169) Aztreonam (p.48) Cefmatilen ( p. 110) Cefuzonam (p. 171) Bacampicillin (p. 50) Cefmetazole (p. 112) Cefalexin (p. 173) Bacitracin (p. 52) Cefodizime (p. 114) Chloramphenicol (p.175) Balofloxacin (p. 54) Cefonicid (p. 116) Cilastatin (p. 177) Carbenicillin (p. 56) Cefoperazone (p. 118) Ciprofloxacin (p. 179) Cefacetrile (p. 58) Cefoselis (p. 120) Clarithromycin (p. 181) Cefaclor (p. 60) Cefotaxime (p. 122) Clinafloxacin (p. 183) Cefadroxil (p. 62) Cefotetan (p. 124) Clindamycin (p. 185) Cefalogycin (p. 64) Cefoxazole (p. 126) Clofazimine (p. 187) Cefaloram (p. 66) Cefozopran (p. 128) Cloxacillin (p. 189) Cefaloridine (p. 68) Cefpimizole (p. 130) Cycloserine (p. 191) Cefamandole (p. 70) Cefpirome (p. 132) Dapsone (p. 193) Cefaparole (p. 72) Cefprozil (p. 134) Daptomycin (p. 195) Cefapirin (p. 74) Cefquinome (p. 136) Demeclocycline (p. 197) Cefatrizine (p. 76) Cefradine (cephradine) Dicloxacillin (p. 199) Cefazaflur (p. 78) ( p. 138) Dirithromycin (p. 201) Cefazedone (p. 80) Cefrotil (p. 141) Doripenem (p. 203) Cefazolin (p. 82) Cefroxadine (p. 143) Doxorubicin (p. 205) Cefcanel (p. 84) Ceftaroline fosamil (p. 145) Doxycycline (p. 207) Cefcapene (p. 86) Ceftazidime (p. 147) Enoxacin (p. 209) Cefclidine (p. 88) Cefteram (p. 149) Ertapenem (p. 211) Cefdaloxime (p. 90) Ceftezole (p. 151) Erythromycin (p. 213) Cefdinir (p. 92) Ceftibuten (p. 153) Ethambutol (p. 215) Cefditoren (p. 94) Ceftiofur (p. 155) Ethionamide (p. 217) Cefedrolor (p. 96) Ceftiolene (p. 157) Fidaxomicin (p. 219) Computational Antibiotics Flucloxacillin (p. 221) Nitrofurantoin (p. 286) Silversulfadiazine (p. 352) Flumequine (p. 223) Norfloxcin (p. 288) Sitafloxacin (p. 354) Furazolidone (p. 225) Ofloxacin (p. 290) Spartfloxacin (p. 356) Fusidic Acid (p. 227) Oxacillin (p. 292) Spectinomycin (p. 358) Gatifloxacin (p. 229) Oxolinic Acid (p. 295) Spiramycin (p. 360) Geldanamycin (p. 231) Oxytetracyline (p. 297) Streptomycin (p. 363) Gemifloxacin (p. 233) Paromomycin (p. 299) Sulfacetamide (p. 366) Gentamicin (p. 235) Pazufloxacin (p. 301) Sulfadiazine (p. 368) Grepafloxacin (p. 237) Penicillin G (p. 303) Sulfaethizole (p. 370) Herbimycin (p. 239) Penicillin V (p. 305) Sulfamethoxazole (p. 372) Imipenem (p. 241) Pefloxacin (p. 307) Sulfanilamide (p. 374) Kanamycin (p. 244) Pivmecillinam (p. 309) Sulfasalazine (p. 376) Keflin (p. 246) Pipemidic acid (p. 311) Sulfisoxazole (p. 378) Levofloxacin (p. 248) Piperacillin (p. 313) Torezolid (p. 380) Lincomycin (p. 250) Piromidic Acid (p. 315) Teflaro (Ceftaroline) (p. 382) Linezolid (p. 252) Pivampicillin (p. 317) Teicoplanin (p. 384) Lomefloxacin (p. 254) Platensimycin (p. 320) Telavancin (p. 386) Loracarbef (p. 256) Polymyxin B (p. 322) Telithromycin (p. 388) Mefoxin (p. 258) Posizolid (p. 324) Temafloxacin (p. 391) Meropenem (p. 260) Pristinamycin (p. 326) Temocillin (p. 393) Metamide (p. 262) Prulifloxacin (p. 328) Tetracycline (p. 395) Methicillin (p. 264) Pyrozinamide (p. 330) Thiamphenicol (p. 397) Metronidazole (p. 266) Quinupristin (p. 332) Ticarcillin (p. 399) Mezlocillin (p. 268) Radezolid (p. 334) Tigecycline (p. 401) Minocycline (p. 270) Rifabutin (p. 336) Tinidazol (p. 403) Moxifloxacin (p. 272) Rifampin (p. 338) Tobramycin (p. 405) Mupirocin (p. 274) Rifapentine (p. 340) Troleandomycin (p. 407) Nadifloxacin (p. 276) Rifaximin (p. 342) Trovafloxacin (p. 409) Nafcillin (p. 278) Rosoxacin (p. 344) Vancomycin (p. 411) Nalidixic acid (p. 280) Roxarsone (p. 346) Viomycin (p. 414) Neomycin (p. 282) Roxithromycin (p. 348) Besifloxacin (p. 416) Netilmicin (p. 284) Rufloxacin (p. 350) Cefmenoxime (p. 418) Computational Antibiotics Graph 1: Molar mass vs. total polar surface area (TPSA) (p. 420) Graph 2: Dipole moment vs. total polar surface area (TPSA) (p.421) Graph 3: Total polar surface area vs. molecular volume (p.422) Graph 4: Total polar surface area vs. number of hydrogen bond donors (p.423) Graph 5: Total polar surface area vs. number of hydrogen bond acceptors (p.423) Graph 6: Total polar surface area vs. surface area (p.424) Graph 7: Total polar surface area vs. number of rotatable bonds (p.425) Graph 8: Total polar surface area vs. ratio of dipole to molecular volume (D/V) (p.426) Graph 9: Total polar surface area vs. mlog P (p.427) Graph 10: Molar mass vs. dipole moment (p.428) Graph 11: Molar mass vs. molar volume (p.429) Graph 12: Molar mass vs. number of hydrogen bond donors (p.430) Graph 13: Molar mass vs. surface area (p.431) Graph 14: Molar mass vs. number of hydrogen bond acceptors (p.432) Graph 15: Molar mass vs. number of rotational bonds (p.432) Graph 16: Molar mass vs. ratio of dipole to molecular volume (D/V) (p.434) Graph 17: mlog P vs. molar mass (p.435) Graph 18: Dipole moment vs. molecular volume (p.436) Graph 19: Dipole moment vs. number of hydrogen bond donors (p.437) Graph 20: Dipole moment vs. number of hydrogen bond acceptors (p.438) Graph 21: Dipole moment vs. surface area (p.439) Graph 22: Dipole moment vs. number of rotatable bonds (p.440) Graph 23: Ratio of dipole moment to molecular volume (D/V) vs. number of rotational bonds (p.441 Graph 24: Number of rotatable bonds vs. mlog P (p.442) Graph 25: Molecular volume vs. number of hydrogen bond donors (p.443) Computational Antibiotics Graph 26: Molecular volume vs. number of hydrogen bond acceptors (p.444) Graph 27: Molecular volume vs. surface area (p.445) Graph 28: Number of rotatable bonds vs. molecular volume (p.446) Graph 29: Dipole moment vs. molecular volume (p.447) Graph 30: Molecular volume vs. mlog P (p. 448) Graph 31: Number of hydrogen bond donors vs. number of hydrogen bond acceptors (p. 449) Graph 32: Number of hydrogen bond donors vs. surface area (p. 450) Graph 33: Number of hydrogen bond donors vs. number of rotatable bonds (p. 451) Graph 34: Ratio of dipole moment to molecular volume (D/V) vs. number of hydrogen bond donors (p. 452) Graph 35: mlog P vs. hydrogen bonds donor (p. 453) Graph 36: Surface area vs. number of hydrogen bond acceptors (p. 454) Graph 37: Number of rotatable bonds vs. hydrogen bond acceptors (p. 455) Graph 38: Dipole moment vs. number of hydrogen bond acceptors (p. 456) Graph 39: mlog P vs. number of hydrogen bond acceptors (p. 457) Graph 40: Number of rotatable bonds vs. surface area (p. 458) Graph 41: Ratio of dipole to molecular volume (D/V) vs. surface area (p. 459) Graph 42: mlog P vs. surface area (p. 460) Graph 43: Number of rotatable bonds vs. ration of dipole to molecular volume (D/V) (p. 461) Graph 44: Number of rotatable bonds vs. mlog P (p. 462) Graph 45: Dipole moment vs. molecular volume (p. 463) Computational Antibiotics Computational Details Each of the molecules in this compilation can be downloaded from the web site http://antibiotics.valdosta.edu Using the password “antibiotic” (no quotes). This project was conducted using Spartan Cluster (Wavefunction) software. Structural parameters were calculated using Semi empirical PM3 (neutral). Additional ions that might be present in the actual pharmaceutical agents (sulfate, chloride, etc.) were not included in the structures or calculations. Molinspiration (http://www.molinspiration.com/services/properties.html) was used to calculate parameters such as number of rotatable bonds, logP (water-octanol partition coefficient), TPSA, etc. These are parameters linked to Lipinski’s Rules. Each page contains some additional information about the molecules including different names, cell line and clinical studies and some review papers that may be available on the web. These are by no means to be considered a complete list of citations. This book and website are the result of a class project in a CHEM4920 class entitled “Antibiotics”. Note the page numbers are approximate as the *.pdf compilation can shift the files while combining into a single document. Computational Antibiotics ACKNOWLEDGEMENTS We would like to thank several divisions and individuals at Valdosta State University (www.valdosta.edu, Valdosta, Ga.). The Information Technology Division is thanked for maintaining the chemistry department computer lab and cluster where much of this work was performed. Also, the installation
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