De novo computational design of compounds virtually displaying potent antibacterial activity and desirable in vitro ADMET profiles

Alonso N, Caamano O, Romero-Duran FJ, Luan F, Cordeiro MNDS, Yanez M, Gonzalez-Diaz H, Garcia-Mera X (2013) Model for high-throughput screening of multitarget drugs in chemical neurosciences: synthesis, assay, and theoretic study of rasagiline carbamates. ACS Chem Neurosci 4(10):1393–1403

Baskin II, Skvortsova MI, Stankevich IV, Zefirov NS (1995) On the basis of invariants of labeled molecular graphs. J Chem Inf Comput Sci 35(3):527–531

Borchardt RT, Kerns EH, Hageman MJ, Thakker DR, Stevens JL (eds) (2006) Optimizing the “Drug-Like” Properties of Leads in Drug Discovery, vol IV. Biotechnology: Pharmaceutical Aspects, Springer Science+Business Media, LLC, New York, NY

Brachman PS, Abrutyn E (2009) Bacterial Infections of Humans: Epidemiology and Control. Springer Science+Business Media, LLC, New York, NY

CambridgeSoft (2003) ChemDraw Ultra.v8.0, PerkinElmer, Inc., Cambridge, MA

Carloni P, Alber F (eds) (2003) Quantum Medicinal Chemistry, vol 17. Methods and Principles in Medicinal Chemistry. WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

Carrio P, Pinto M, Ecker G, Sanz F, Pastor M (2014) Applicability Domain ANalysis (ADAN): a robust method for assessing the reliability of drug property predictions. J Chem Inf Model 54(5):1500–1511

Croes S, Koop AH, van Gils SA, Neef C (2012) Efficacy, nephrotoxicity and ototoxicity of aminoglycosides, mathematically modelled for modelling-supported therapeutic drug monitoring. Eur J Pharm Sci 45(1-2):90–100

ChemAxon (1998–2016) Standardizer (Tool for structure canonicalization and transformation), JChem.v15.11.16.0, ChemAxon, Budapest, Hungary

Doucet JP, Weber J (1996) Computer-aided molecular design: Theory and applications. Academic Press, London, San Diego, New York, NY, Boston, Sidney, Tokyo, Toronto

Estrada E (1999) Novel strategies in the search of topological indices. In: Devillers J, Balaban AT (eds) Topological Indices and Related Descriptors in QSAR and QSPR. Gordon and Breach Science Publishers, Amsterdam, p 403–453

Estrada E, Peña A (2000) In silico studies for the rational discovery of anticonvulsant compounds. Bioorg Med Chem 8(12):2755–2770

Estrada E, Uriarte E, Montero A, Teijeira M, Santana L, De Clercq E (2000) A novel approach for the virtual screening and rational design of anticancer compounds. J Med Chem 43(10):1975–1985

Gaspar HA, Marcou G, Horvath D, Arault A, Lozano S, Vayer P, Varnek A (2013) Generative topographic mapping-based classification models and their applicability domain: application to the biopharmaceutics Drug Disposition Classification System (BDDCS). J Chem Inf Model 53(12):3318–3325

Gaulton A, Bellis LJ, Bento AP, Chambers J, Davies M, Hersey A, Light Y, McGlinchey S, Michalovich D, Al-Lazikani B, Overington JP (2012) ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic Acids Res 40:D1100–1107. Database issue

Ghose AK, Viswanadhan VN, Wendoloski JJ (1999) A knowledge-based approach in designing combinatorial or medicinal chemistry libraries for drug discovery. 1. A qualitative and quantitative characterization of known drug databases. J Comb Chem 1(1):55–68

Gubernator K, James CA, Gubernator N (2005) eMolecules. Available at: https://www.emolecules.com/ . Accessed 15 Dec 2016

Hau J, Schapiro SJ (2011) Handbook of Laboratory Animal Science: Essential Principles and Practices. CRC Press, Taylor & Francis Group, LLC, Boca Raton, FL

Hill T, Lewicki P (2006) STATISTICS methods and applications. A comprehensive reference for science, industry and data mining. StatSoft, Tulsa

Irwin JJ, Shoichet BK (2005) ZINC–a free database of commercially available compounds for virtual screening. J Chem Inf Model 45(1):177–182

Jahnke W, Erlanson DA (2006) Fragment-based approaches in drug discovery. Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany

Kaiser J (2005) Science resources. Chemists want NIH to curtail database. Science 308(5723):774

Kaye KS, Pogue JM (2015) Infections caused by resistant Gram-negative bacteria: Epidemiology and management. Pharmacotherapy 35(10):949–962

Klein CD, Hopfinger AJ (1998) Pharmacological activity and membrane interactions of antiarrhythmics: 4D-QSAR/QSPR analysis. Pharm Res 15(2):303–311

Kubinyi H, Folkers G, Martin YC (eds) (2002) 3D QSAR in Drug Design: Recent Advances, vol 3. Kluwer Academic Publishers, New York, NY, Boston, Dordrecht, London, Moscow

Lipinski CA, Lombardo F, Dominy BW, Feeney PJ (2001) Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev 46(1-3):3–26

Luan F, Cordeiro MNDS, Alonso N, Garcia-Mera X, Caamano O, Romero-Duran FJ, Yanez M, Gonzalez-Diaz H (2013) TOPS-MODE model of multiplexing neuroprotective effects of drugs and experimental-theoretic study of new 1,3-rasagiline derivatives potentially useful in neurodegenerative diseases. Bioorg Med Chem 21(7):1870–1879

Mok NY, Brenk R (2011) Mining the ChEMBL database: an efficient chemoinformatics workflow for assembling an ion channel-focused screening library. J Chem Inf Model 51(10):2449–2454

Moriguchi I, Hirono S, Liu Q, Nakagome I, Matsushita Y (1992) Simple method of calculating octanol/water partition coefficient. Chem Pharm Bull 40(1):127–130

Overington J (2009) ChEMBL. An interview with John Overington, team leader, chemogenomics at the European bioinformatics institute outstation of the European molecular biology laboratory (EMBL-EBI). Interview by Wendy A. Warr. J Comput Aided Mol Des 23(4):195–198

Paul SM, Mytelka DS, Dunwiddie CT, Persinger CC, Munos BH, Lindborg SR, Schacht AL (2010) How to improve R&D productivity: the pharmaceutical industry’s grand challenge. Nat Rev Drug Discov 9(3):203–214

Pearson K (1895) Notes on regression and inheritance in the case of two parents. Proc R Soc Lond 58:240–242

Prado-Prado FJ, Garcia-Mera X, Gonzalez-Diaz H (2010) Multi-target spectral moment QSAR versus ANN for antiparasitic drugs against different parasite species. Bioorg Med Chem 18(6):2225–2231

Romero-Duran FJ, Alonso N, Yanez M, Caamano O, Garcia-Mera X, Gonzalez-Diaz H (2016) Brain-inspired cheminformatics of drug-target brain interactome, synthesis, and assay of TVP1022 derivatives. Neuropharmacology 103:270–278

Romero Duran FJ, Alonso N, Caamano O, Garcia-Mera X, Yanez M, Prado-Prado FJ, Gonzalez-Diaz H (2014) Prediction of multi-target networks of neuroprotective compounds with entropy indices and synthesis, assay, and theoretical study of new asymmetric 1,2-rasagiline carbamates. Int J Mol Sci 15(9):17035–17064

Ryan KJ, Ray CG (2004) Sherris Medical Microbiology. An Introduction to infectious diseases. McGraw-Hill Companies, Inc, Arizona

Sahigara F, Mansouri K, Ballabio D, Mauri A, Consonni V, Todeschini R (2012) Comparison of different approaches to define the applicability domain of QSAR models. Molecules 17(5):4791–4810

Speck-Planche A, Cordeiro MNDS (2013) Simultaneous modeling of antimycobacterial activities and ADMET profiles: a chemoinformatic approach to medicinal chemistry. Curr Top Med Chem 13(14):1656–1665

Speck-Planche A, Cordeiro MNDS (2014a) Chemoinformatics for medicinal chemistry: in silico model to enable the discovery of potent and safer anti-cocci agents. Future Med Chem 6(18):2013–2028

Speck-Planche A, Cordeiro MNDS (2014b) Simultaneous virtual prediction of anti-Escherichia coli activities and ADMET profiles: A chemoinformatic complementary approach for high-throughput screening. ACS Comb Sci 16(2):78–84

Speck-Planche A, Kleandrova VV, Cordeiro MNDS (2013a) New insights toward the discovery of antibacterial agents: Multi-tasking QSBER model for the simultaneous prediction of anti-tuberculosis activity and toxicological profiles of drugs. Eur J Pharm Sci 48(4-5):812–818

Speck-Planche A, Kleandrova VV, Luan F, Cordeiro MNDS (2013b) Unified multi-target approach for the rational in silico design of anti-bladder cancer agents. Anticancer Agents Med Chem 13(5):791–800

Speck-Planche A, Kleandrova VV, Ruso JM, Cordeiro MNDS (2016) First multitarget chemo-bioinformatic model to enable the discovery of antibacterial peptides against multiple Gram-positive pathogens. J Chem Inf Model 56(3):588–598

Statsoft-Team (2001) STATISTICA. Data analysis software system.v6.0, Tulsa

Talete-srl (2015) DRAGON (Software for Molecular Descriptor Calculation).v6.0, http://www.talete.mi.it/

Tenorio-Borroto E, Penuelas-Rivas CG, Vasquez-Chagoyan JC, Castanedo N, Prado-Prado FJ, Garcia-Mera X, Gonzalez-Diaz H (2014) Model for high-throughput screening of drug immunotoxicity - Study of the anti-microbial G1 over peritoneal macrophages using flow cytometry. Eur J Med Chem 72:206–220

Tenorio-Borroto E, Penuelas Rivas CG, Vasquez Chagoyan JC, Castanedo N, Prado-Prado FJ, Garcia-Mera X, Gonzalez-Diaz H (2012) ANN multiplexing model of drugs effect on macrophages; theoretical and flow cytometry study on the cytotoxicity of the anti-microbial drug G1 in spleen. Bioorg Med Chem 20(20):6181–6194

Toplak M, Mocnik R, Polajnar M, Bosnic Z, Carlsson L, Hasselgren C, Demsar J, Boyer S, Zupan B, Stalring J (2014) Assessment of machine learning reliability methods for quantifying the applicability domain of QSAR regression models. J Chem Inf Model 54(2):431–441

Valdés-Martini JR, García-Jacas CR, Marrero-Ponce Y, Silveira Vaz ‘d Almeida Y, Morell C (2012) QUBILs-MAS: Free software for molecular descriptors calculator from quadratic, bilinear and linear maps based on graph-theoretic electronic-density matrices and atomic weightings.v1.0, Villa Clara, http://tomocomd.com/

Vasoo S, Barreto JN, Tosh PK (2015) Emerging issues in gram-negative bacterial resistance: an update for the practicing clinician. Mayo Clin Proc 90(3):395–403

Veber DF, Johnson SR, Cheng HY, Smith BR, Ward KW, Kopple KD (2002) Molecular properties that influence the oral bioavailability of drug candidates. J Med Chem 45(12):2615–2623

Vedani A, Dobler M (2002) 5D-QSAR: the key for simulating induced fit? J Med Chem 45(11):2139–2149

Vedani A, Dobler M, Lill MA (2005) Combining protein modeling and 6D-QSAR. Simulating the binding of structurally diverse ligands to the estrogen receptor. J Med Chem 48(11):3700–3703

Williams AJ (2011) Chemspider: a platform for crowdsourced collaboration to curate data derived from public compound databases. In: Ekins S, Hupcey MAZ, Williams AJ (eds) Collaborative computational technologies for biomedical research. John Wiley & Sons, Inc., Hoboken, NJ, p 363–386