In silico comparison of marine, terrestrial and synthetic compounds using ChemGPS-NP for navigating chemical space

LIII. On lines and planes of closest fit to systems of points in space

Karl Pearson, F. R. S. (1901) · The London Edinburgh and Dublin Philosophical Magazine and Journal of Science · doi:10.1080/14786440109462720 · Cited by 13,658 · see citing works

Principal component analysis

Wold, S., Esbensen, K. H., & Geladi, P. L. M. (1987) · Chemometrics and Intelligent Laboratory Systems · doi:10.1016/0169-7439(87)80084-9 · Cited by 11,792 · see citing works

SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules

Weininger, D. (1988) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci00057a005 · Cited by 7,436 · see citing works

Natural products as sources of new drugs over the last 25 years

Newman, D. J., & Cragg, G. M. (2007) · Journal of Natural Products · doi:10.1021/np068054v · Cited by 5,517 · see citing works

Marine natural products

Faulkner, D. J. (1990) · Natural Product Reports · doi:10.1039/np9900700269 · Cited by 4,880 · see citing works

Orthogonal projections to latent structures (O‐PLS)

Trygg, J., & Wold, S. (2002) · Journal of Chemometrics · doi:10.1002/cem.695 · Cited by 2,489 · see citing works

OPLS discriminant analysis: combining the strengths of PLS-DA and SIMCA classification

Bylesjö, M., Rantalainen, M., Cloarec, O., Nicholson, J. K., Holmes, E., & Trygg, J. (2006) · Journal of Chemometrics · doi:10.1002/cem.1006 · Cited by 1,475 · see citing works

The influence of natural products upon drug discovery (Antiquity to late 1999)

Newman, D. J., Cragg, G. M., & Snader, K. M. (2000) · Natural Product Reports · doi:10.1039/a902202c · Cited by 1,293 · see citing works

Visualization of GC/TOF-MS-Based Metabolomics Data for Identification of Biochemically Interesting Compounds Using OPLS Class Models

Wiklund, S., Johansson, E., Sjöström, L., Mellerowicz, E. J., Edlund, U. G., Shockcor, J. P., Gottfries, J., Möritz, T., & Trygg, J. (2007) · Analytical Chemistry · doi:10.1021/ac0713510 · Cited by 1,234 · see citing works

Lessons from natural molecules

Clardy, J., & Walsh, C. T. (2004) · Nature · doi:10.1038/nature03194 · Cited by 1,178 · see citing works

Navigating chemical space for biology and medicine

Lipinski, C. A., & Hopkins, A. L. (2004) · Nature · doi:10.1038/nature03193 · Cited by 1,008 · see citing works

Chemical space and biology

Dobson, C. M. (2004) · Nature · doi:10.1038/nature03192 · Cited by 1,003 · see citing works

Property Distributions: Differences between Drugs, Natural Products, and Molecules from Combinatorial Chemistry

Fehér, M., & Schmidt, J. M. (2002) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci0200467 · Cited by 926 · see citing works

Drugs from the deep: Marine natural products as drug candidates

Haefner, B. (2003) · Drug Discovery Today · doi:10.1016/s1359-6446(03)02713-2 · Cited by 740 · see citing works

Drug discovery from natural sources

Chin, Y., Balunas, M. J., Chai, H. B., & Kinghorn, A. D. (2006) · The AAPS Journal · doi:10.1007/bf02854894 · Cited by 692 · see citing works

The impact of natural products upon modern drug discovery

Ganesan, A. (2008) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2008.03.016 · Cited by 653 · see citing works

Drugs from the seas - current status and microbiological implications

Proksch, P., Edrada‐Ebel, R., & Ebel, R. (2002) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-002-1006-8 · Cited by 572 · see citing works

Marine pharmacology in 2005–6: Marine compounds with anthelmintic, antibacterial, anticoagulant, antifungal, anti-inflammatory, antimalarial, antiprotozoal, antituberculosis, and antiviral activities; affecting the cardiovascular, immune and nervous systems, and other miscellaneous mechanisms of action

Mayer, A. M. S., Rodrı́guez, A. D., Berlinck, R. G. S., & Hamann, M. T. (2009) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2009.03.011 · Cited by 458 · see citing works

Marine natural products

Faulkner, D. J. (2001) · Natural Product Reports · doi:10.1039/b009029h · Cited by 409 · see citing works

Chemography: The Art of Navigating in Chemical Space

Oprea, T. I., & Gottfries, J. (2001) · Journal of Combinatorial Chemistry · doi:10.1021/cc0000388 · Cited by 351 · see citing works

Natural products and combinatorial chemistry: back to the future

Ortholand, J., & Ganesan, A. (2004) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2004.04.011 · Cited by 337 · see citing works

Protein flexibility and drug design: how to hit a moving target

Carlson, H. A. (2002) · Current Opinion in Chemical Biology · doi:10.1016/s1367-5931(02)00341-1 · Cited by 314 · see citing works

Effects of Astaxanthin on Lipopolysaccharide-Induced Inflammation In Vitro and In Vivo

Ohgami, K., Shiratori, K., Kotake, S., Nishida, T., Mizuki, N., Yazawa, K., & Ohno, S. (2003) · Investigative Ophthalmology & Visual Science · doi:10.1167/iovs.02-0822 · Cited by 307 · see citing works

Marine natural products

Blunt, J. W., Copp, B. R., Munro, M. H. G., Northcote, P. T., & Prinsep, M. R. (2004) · Natural Product Reports · doi:10.1039/b305250h · Cited by 298 · see citing works

Novel Chemical Space Exploration via Natural Products

Rosén, J., Gottfries, J., Mureşan, S., Backlund, A., & Oprea, T. I. (2009) · Journal of Medicinal Chemistry · doi:10.1021/jm801514w · Cited by 284 · see citing works

ChemInform Abstract: Marine Natural Products

Faulkner, D. J. (1995) · ChemInform · doi:10.1002/chin.199504291 · Cited by 272 · see citing works

The Question of the Existence of Specific Marine Bacteria1

MacLeod, R. A. (1965) · Bacteriological Reviews · doi:10.1128/mmbr.29.1.9-23.1965 · Cited by 221 · see citing works

Secondary metabolites from marine microorganisms

Kelecom, A. G. A. C. (2002) · Anais da Academia Brasileira de Ciências · doi:10.1590/s0001-37652002000100012 · Cited by 210 · see citing works

ChemGPS-NP: Tuned for Navigation in Biologically Relevant Chemical Space

Larsson, J., Gottfries, J., Mureşan, S., & Backlund, A. (2007) · Journal of Natural Products · doi:10.1021/np070002y · Cited by 209 · see citing works

Natural Products Chemistry in the Marine Environment

Fenical, W. (1982) · Science · doi:10.1126/science.215.4535.923 · Cited by 205 · see citing works

Marine pharmacology in 2001–2002: Marine compounds with anthelmintic, antibacterial, anticoagulant, antidiabetic, antifungal, anti-inflammatory, antimalarial, antiplatelet, antiprotozoal, antituberculosis, and antiviral activities; affecting the cardiovascular, immune and nervous systems and other miscellaneous mechanisms of action

Mayer, A. M. S., & Hamann, M. T. (2005) · Comparative Biochemistry and Physiology Part C Toxicology & Pharmacology · doi:10.1016/j.cca.2005.04.004 · Cited by 182 · see citing works

Chemical Ecology of Marine Microbial Defense

Engel, S., Jensen, P. R., & Fenical, W. (2002) · Journal of Chemical Ecology · doi:10.1023/a:1020793726898 · Cited by 178 · see citing works

The Role of Pharmacognosy in Modern Medicine and Pharmacy

Jones, W., Chin, Y., & Kinghorn, A. D. (2006) · Current Drug Targets · doi:10.2174/138945006776054915 · Cited by 166 · see citing works

Megavariate analysis of environmental QSAR data. Part I – A basic framework founded on principal component analysis (PCA), partial least squares (PLS), and statistical molecular design (SMD)

Eriksson, L., Andersson, P. L., Johansson, E., et al. (2006) · Molecular Diversity · doi:10.1007/s11030-006-9024-6 · Cited by 162 · see citing works

Marine pharmacology in 2003–4: Marine compounds with anthelmintic antibacterial, anticoagulant, antifungal, anti-inflammatory, antimalarial, antiplatelet, antiprotozoal, antituberculosis, and antiviral activities; affecting the cardiovascular, immune and nervous systems, and other miscellaneous mechanisms of action

Mayer, A. M. S., Rodrı́guez, A. D., Berlinck, R. G. S., & Hamann, M. T. (2007) · Comparative Biochemistry and Physiology Part C Toxicology & Pharmacology · doi:10.1016/j.cbpc.2007.01.015 · Cited by 157 · see citing works

New Manzamine Alkaloids with Activity against Infectious and Tropical Parasitic Diseases from an Indonesian Sponge

Rao, K. V., Santarsiero, B. D., Mesecar, A. D., Schinazi, R. F., Tekwani, B. L., & Hamann, M. T. (2003) · Journal of Natural Products · doi:10.1021/np020592u · Cited by 155 · see citing works

Clinical status of anti-cancer agents derived from marine sources

Singh, R., Sharma, M., Joshi, P., & Rawat, D. (2008) · Anti-Cancer Agents in Medicinal Chemistry · doi:10.2174/187152008785133074 · Cited by 143 · see citing works

Properties and Architecture of Drugs and Natural Products Revisited

Grabowski, K., & Schneider, G. (2007) · Current Chemical Biology · doi:10.2174/2212796810701010115 · Cited by 132 · see citing works

Antiviral activity of diterpenes isolated from the Brazilian marine alga Dictyota menstrualis against human immunodeficiency virus type 1 (HIV-1)

Pereira, H. D. S., Leão-Ferreira, L. R., Moussatché, N., Teixeira, V. L., Cavalcanti, D. N., COSTA, L., Diaz, R. S., & FRUGULHETTI, I. (2004) · Antiviral Research · doi:10.1016/j.antiviral.2004.06.006 · Cited by 128 · see citing works

Nagelamides A−H, New Dimeric Bromopyrrole Alkaloids from Marine Sponge Agelas Species

Endo, T., Tsuda, M., Okada, T., et al. (2004) · Journal of Natural Products · doi:10.1021/np034077n · Cited by 119 · see citing works

Clinical Status of Anti-Cancer Agents Derived from Marine Sources

Singh, R. K., Sharma, M. M., Joshi, P., et al. (2008) · Anti-Cancer Agents in Medicinal Chemistry · doi:10.2174/1871520610808060603 · Cited by 106 · see citing works

ChemGPS-NPWeb: chemical space navigation online

Rosén, J., Lövgren, A., Kogej, T., Mureşan, S., Gottfries, J., & Backlund, A. (2008) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-008-9255-y · Cited by 102 · see citing works

Natural Products as Aromatase Inhibitors

Balunas, M. J., Su, B., Brueggemeier, R. W., & Kinghorn, A. D. (2008) · Anti-Cancer Agents in Medicinal Chemistry · doi:10.2174/187152008785133092 · Cited by 102 · see citing works

Distinguishing between Natural Products and Synthetic Molecules by Descriptor Shannon Entropy Analysis and Binary QSAR Calculations

Stahura, F. L., Godden, J. W., Xue, L., & Bajorath, J. (2000) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci0003303 · Cited by 101 · see citing works

Plicatamide, an Antimicrobial Octapeptide from Styela plicata Hemocytes

Tincu, J. A., Menzel, L. P., Azimov, R., Sands, J., Hong, T., Waring, A. J., Taylor, S. W., & Lehrer, R. I. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m211332200 · Cited by 92 · see citing works

Expanding the ChemGPS Chemical Space with Natural Products

Larsson, J., Gottfries, J., Bohlin, L., et al. (2005) · Journal of Natural Products · doi:10.1021/np049655u · Cited by 79 · see citing works

A Marine Natural Product Database

Lei, J., & Zhou, J. (2002) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci010111x · Cited by 68 · see citing works

Biodiversity, chemical diversity and drug discovery

Singh, S. B., & Peláez, F. (2007) · Birkhäuser Basel eBooks · doi:10.1007/978-3-7643-8117-2_4 · Cited by 66 · see citing works

Structure and Stereochemistry of a New Cytotoxic Polychlorinated Sulfolipid from Adriatic Shellfish

Ciminiello, P., Dell’Aversano, C., Fattorusso, E., et al. (2002) · Journal of the American Chemical Society · doi:10.1021/ja0207347 · Cited by 66 · see citing works

Anti-adhesive glycoproteins in echinoderm mucus secretions

Bavington, C. D., Lever, R., Mulloy, B., et al. (2004) · Comparative Biochemistry and Physiology Part B Biochemistry and Molecular Biology · doi:10.1016/j.cbpc.2004.07.008 · Cited by 58 · see citing works

Unlocking Interpretation in Near Infrared Multivariate Calibrations by Orthogonal Partial Least Squares

Stenlund, H. C., Johansson, E., Gottfries, J., et al. (2008) · Analytical Chemistry · doi:10.1021/ac801803e · Cited by 51 · see citing works

Mololipids, A New Series of Anti-HIV Bromotyramine-Derived Compounds from a Sponge of the Order Verongida

Ross, S. A., Weete, J. D., Schinazi, R. F., et al. (2000) · Journal of Natural Products · doi:10.1021/np980414u · Cited by 49 · see citing works

New sesterterpenes from Madagascan Lendenfeldia sponges

Chill, L., Rudi, A., Aknin, M., et al. (2004) · Tetrahedron · doi:10.1016/j.tet.2004.09.022 · Cited by 49 · see citing works

Modulatory Effect of Bolinaquinone, a Marine Sesquiterpenoid, on Acute and Chronic Inflammatory Processes

Lucas-Domínguez, R., Giannini, C., D’Auria, M. V., & Payá, M. (2003) · Journal of Pharmacology and Experimental Therapeutics · doi:10.1124/jpet.102.045278 · Cited by 45 · see citing works

Bryostatin 1 modulates β-catenin subcellular localization and transcription activity through protein kinase D1 activation

Jaggi, M., Chauhan, S. C., Du, C., & Balaji, K. C. (2008) · Molecular Cancer Therapeutics · doi:10.1158/1535-7163.mct-08-0119 · Cited by 36 · see citing works

Marine cytotoxic macrolides haterumalides and biselides, and related natural products

Kigoshi, H., & Hayakawa, I. (2007) · The Chemical Record · doi:10.1002/tcr.20119 · Cited by 35 · see citing works

Combinatorial Synthesis of Natural Product-Based Libraries

(2006) · CRC Press eBooks · doi:10.1201/9781420009279 · Cited by 35 · see citing works

Reversal of Fluconazole Resistance in Multidrug Efflux-Resistant Fungi by the Dysidea arenaria Sponge Sterol 9α,11α-Epoxycholest-7-ene-3β,5α,6α,19-tetrol 6-Acetate

Jacob, M. R., Hossain, C. F., Mohammed, K. A., et al. (2003) · Journal of Natural Products · doi:10.1021/np030317n · Cited by 35 · see citing works

Esmodil: An Acetylcholine Mimetic Resurfaces in a Southern Australian Marine Sponge Raspailia ( Raspailia ) SP

Capon, R. J., Skene, C. E., Liu, E. H., et al. (2004) · Natural Product Research · doi:10.1080/14786410310001620619 · Cited by 33 · see citing works

Secondary Metabolites from Marine Organisms

Rinehart, K. L. (2007) · Novartis Foundation symposium · doi:10.1002/9780470514344.ch14 · Cited by 31 · see citing works

Structure Elucidation of a New Antifungal Sterol Sulfate, Sch 575867, from a Deep-Water Marine Sponge(Family: Astroscleridae).

Yang, S., Chan, T., Pomponi, S. A., et al. (2003) · The Journal of Antibiotics · doi:10.7164/antibiotics.56.186 · Cited by 30 · see citing works

Callipeltin A: sodium ionophore effect and tension development in vascular smooth muscle

Trevisi, L., Cargnelli, G., Ceolotto, G., et al. (2004) · Biochemical Pharmacology · doi:10.1016/j.bcp.2004.04.032 · Cited by 22 · see citing works

Inhibition by Aplidine of the aggregation of the prion peptide PrP 106–126 into β-sheet fibrils

Pérez, M., Sadqi, M., Muñoz, V., & Ávila, J. (2003) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/j.bbadis.2003.08.003 · Cited by 20 · see citing works

ChemGPS‐NP Mapping of Chemical Compounds for Prediction of Anticancer Mode of Action

Rosén, J., Rickardson, L., Backlund, A., et al. (2009) · QSAR & Combinatorial Science · doi:10.1002/qsar.200810162 · Cited by 16 · see citing works

Solid-Phase Combinatorial Synthesis Based on Natural Products

Doi, T., & Takahashi, T. (2006) · CRC Press eBooks · doi:10.1201/9781420009279-10 · Cited by 14 · see citing works

Parguerol and Isoparguerol Isolated from the Sea Hare, Aplysia kurodai, Induce Neurite Outgrowth in PC-12 Cells

Tsukamoto, S., Yamashita, Y. T., Yoshida, T., et al. (2004) · Marine Drugs · doi:10.3390/md204170 · Cited by 11 · see citing works

On the impact of uncorrelated variation in regression mathematics

Gottfries, J., Johansson, E., & Trygg, J. (2008) · Journal of Chemometrics · doi:10.1002/cem.1162 · Cited by 7 · see citing works

Bioactive Compounds in the Chemical Defence of Marine Sponges : Structure-Activity Relationships and Pharmacological Targets

Hedner, E. (2007) · KTH Publication Database DiVA (KTH Royal Institute of Technology) · Cited by 5 · see citing works

Untitled work

(1999) · doi:10.1002/(sici)1521-3773(19990301)38:5

Marine Natural Products: A Source of Novel Anticancer Drugs

Khalifa, S. A. M., Elias, N., Farag, M. A., Chen, L., Saeed, A., Hegazy, M.-E. F., Moustafa, M. S., Abd El-Wahed, A., Al-Mousawi, S. M., Musharraf, S. G., et al. (2019) · Marine Drugs · doi:10.3390/md17090491 · Cited by 555 · see citing works

Fragment-based screening with natural products for novel anti-parasitic disease drug discovery

Liu, M., & Quinn, R. J. (2019) · Expert Opinion on Drug Discovery · doi:10.1080/17460441.2019.1653849 · Cited by 29 · see citing works

Chemical Space Mimicry for Drug Discovery

Yuan, W., Jiang, D., Nambiar, D. K., Liew, L. P., Hay, M. P., Bloomstein, J. D., Lu, P., Turner, B. E., Le, Q., Tibshirani, R. J., et al. (2017) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.6b00754 · Cited by 100 · see citing works

Fragment‐based drug discovery—the importance of high‐quality molecule libraries

Bon, M., Bilsland, A. E., Bower, J. F., & McAulay, K. (2022) · Molecular Oncology · doi:10.1002/1878-0261.13277 · Cited by 153 · see citing works

The Growing Importance of Chirality in 3D Chemical Space Exploration and Modern Drug Discovery Approaches for Hit-ID

Silvestri, I. P., & Colbon, P. J. J. (2021) · ACS Medicinal Chemistry Letters · doi:10.1021/acsmedchemlett.1c00251 · Cited by 85 · see citing works

Green Drug Discovery: Novel Fragment Space from the Biomass-Derived Molecule Dihydrolevoglucosenone (CyreneTM)

Dekker, T., Harteveld, J. W., Wágner, G., de Vries, M. C. M., Custers, H., van de Stolpe, A. C., de Esch, I. J. P., & Wijtmans, M. (2023) · Molecules · doi:10.3390/molecules28041777 · Cited by 13 · see citing works