Ligand efficiency and fragment-based drug discovery

Lead- and drug-like compounds: the rule-of-five revolution

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Ligand efficiency: a useful metric for lead selection

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A decade of fragment-based drug design: strategic advances and lessons learned

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Molecular Complexity and Its Impact on the Probability of Finding Leads for Drug Discovery

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The maximal affinity of ligands

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Fragment-based lead discovery

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Fragment-Based Drug Discovery

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Ligand efficiency indices as guideposts for drug discovery

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Virtual Exploration of the Chemical Universe up to 11 Atoms of C, N, O, F: Assembly of 26.4 Million Structures (110.9 Million Stereoisomers) and Analysis for New Ring Systems, Stereochemistry, Physicochemical Properties, Compound Classes, and Drug Discovery

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Fragment-based lead discovery: leads by design

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Ligand Binding Efficiency: Trends, Physical Basis, and Implications

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Profiling drug-like properties in discovery research

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Fragment-Based Drug Design: How Big Is Too Big?

Hajduk, P. J. (2006) · Journal of Medicinal Chemistry · doi:10.1021/jm060511h · Cited by 269 · see citing works

Library Design for Fragment Based Screening

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High-throughput drug discovery: What can we expect from HTS?

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The role of molecular size in ligand efficiency

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Mode of interaction of .beta.-hydroxy-.beta.-methylglutaryl coenzyme A reductase with strong binding inhibitors: compactin and related compounds

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In Silico and Ex Silico ADME Approaches for Drug Discovery

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Identification of “Latent Hits” in Compound Screening Collections

Mestres, J., & Veeneman, G. H. (2003) · Journal of Medicinal Chemistry · doi:10.1021/jm034078c · Cited by 34 · see citing works

The art and practice of structure-based drug design: A molecular modeling perspective

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The ErbB/HER family of protein-tyrosine kinases and cancer

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Improving Drug Candidates by Design: A Focus on Physicochemical Properties As a Means of Improving Compound Disposition and Safety

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Two Decades under the Influence of the Rule of Five and the Changing Properties of Approved Oral Drugs.

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Ligand and Target Discovery by Fragment-Based Screening in Human Cells

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What Do Medicinal Chemists Actually Make? A 50-Year Retrospective

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Structure-based drug design to augment hit discovery

Kalyaanamoorthy, S., & Chen, Y. P. (2011) · Drug Discovery Today · doi:10.1016/j.drudis.2011.07.006 · Cited by 297 · see citing works

Introduction to Fragment-Based Drug Discovery

Erlanson, D. A. (2011) · Topics in current chemistry · doi:10.1007/128_2011_180 · Cited by 269 · see citing works

Ligand efficiency as a guide in fragment hit selection and optimization

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Chemical and structural lessons from recent successes in protein–protein interaction inhibition (2P2I)

Morelli, X., Bourgeas, R., & Roche, P. (2011) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2011.05.024 · Cited by 223 · see citing works

Comparative Assessment of Scoring Functions on an Updated Benchmark: 1. Compilation of the Test Set

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Molecular inflation, attrition and the rule of five

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Expedited mapping of the ligandable proteome using fully functionalized enantiomeric probe pairs

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Setting expectations in molecular optimizations: Strengths and limitations of commonly used composite parameters

Shultz, M. D. (2013) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2013.08.029 · Cited by 175 · see citing works

Impact of Lipophilic Efficiency on Compound Quality

Tarcsay, Á., Nyíri, K., & Keserű, G. M. (2012) · Journal of Medicinal Chemistry · doi:10.1021/jm201388p · Cited by 176 · see citing works

Design and Synthesis of Novel Lactate Dehydrogenase A Inhibitors by Fragment-Based Lead Generation

Ward, R. A., Brassington, C., Breeze, A. L., Caputo, A. T., Critchlow, S. E., Davies, G. M., Goodwin, L., Hassall, G., Greenwood, R. D. R., Holdgate, G. A., et al. (2012) · Journal of Medicinal Chemistry · doi:10.1021/jm201734r · Cited by 170 · see citing works

State-of-the-art strategies for targeting protein–protein interactions by small-molecule inhibitors

Sheng, C., Dong, G., Miao, Z., Zhang, W., & Wang, W. (2015) · Chemical Society Reviews · doi:10.1039/c5cs00252d · Cited by 165 · see citing works

De Novo Drug Design

Hartenfeller, M., & Schneider, G. (2010) · Methods in molecular biology · doi:10.1007/978-1-60761-839-3_12 · Cited by 160 · see citing works

Harnessing Allostery: A Novel Approach to Drug Discovery

Lu, S., Li, S., & Zhang, J. (2014) · Medicinal Research Reviews · doi:10.1002/med.21317 · Cited by 146 · see citing works

Thermodynamics guided lead discovery and optimization

Ferenczy, G. G., & Keserű, G. M. (2010) · Drug Discovery Today · doi:10.1016/j.drudis.2010.08.013 · Cited by 135 · see citing works

Ligand–receptor interaction platforms and their applications for drug discovery

Ye, F. (2012) · Expert Opinion on Drug Discovery · doi:10.1517/17460441.2012.715631 · Cited by 126 · see citing works

Toward the Rational Design of p53-Stabilizing Drugs: Probing the Surface of the Oncogenic Y220C Mutant

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Anopheles gambiae odorant binding protein crystal complex with the synthetic repellent DEET: implications for structure-based design of novel mosquito repellents

Tsitsanou, K. E., Thireou, T. N., Drakou, C. E., Koussis, K., Keramioti, M., Leonidas, D. D., Eliopoulos, E., Iatrou, K., & Zographos, S. E. (2011) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-011-0745-z · Cited by 114 · see citing works

4‐Acyl Pyrroles: Mimicking Acetylated Lysines in Histone Code Reading

Lucas, X., Wohlwend, D., Hügle, M. J., Schmidtkunz, K., Gerhardt, S., Schüle, R., Jung, M., Einsle, O., & Günther, S. (2013) · Angewandte Chemie International Edition · doi:10.1002/anie.201307652 · Cited by 111 · see citing works

Discovery, Design, and Optimization of Isoxazole Azepine BET Inhibitors

Gehling, V. S., Hewitt, M. C., Vaswani, R. G., Leblanc, Y., Côté, A., Nasveschuk, C. G., Taylor, A. M., Harmange, J.-C., Audia, J. E., Pardo, E., et al. (2013) · ACS Medicinal Chemistry Letters · doi:10.1021/ml4001485 · Cited by 105 · see citing works

Ligand efficiency metrics in drug discovery: the pros and cons from a practical perspective

Cavalluzzi, M. M., Mangiatordi, G. F., Nicolotti, O., & Lentini, G. (2017) · Expert Opinion on Drug Discovery · doi:10.1080/17460441.2017.1365056 · Cited by 104 · see citing works

Application of Fragment-Based NMR Screening, X-ray Crystallography, Structure-Based Design, and Focused Chemical Library Design to Identify Novel μM Leads for the Development of nM BACE-1 (β-Site APP Cleaving Enzyme 1) Inhibitors

Wang, Y., Strickland, C., Voigt, J. H., Kennedy, M. E., Beyer, B. M., Senior, M. M., Smith, E. M., Nechuta, T. L., Madison, V., Czarniecki, M., et al. (2009) · Journal of Medicinal Chemistry · doi:10.1021/jm901472u · Cited by 103 · see citing works

The thermodynamic basis for the use of lipophilic efficiency (LipE) in enthalpic optimizations

Shultz, M. D. (2013) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2013.08.030 · Cited by 101 · see citing works

Evolving molecules using multi-objective optimization: applying to ADME/Tox

Ekins, S., Honeycutt, J. D., & Metz, J. T. (2010) · Drug Discovery Today · doi:10.1016/j.drudis.2010.04.003 · Cited by 102 · see citing works

The impact of in silico screening in the discovery of novel and safer drug candidates

Rognan, D. (2017) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2017.02.034 · Cited by 99 · see citing works

A general fragment-based approach to identify and optimize bioactive ligands targeting RNA

Suresh, B. M., Li, W., Zhang, P., Wang, K. W., Yildirim, I., Parker, C. G., & Disney, M. D. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2012217117 · Cited by 100 · see citing works

Strategies for targeting undruggable targets

Zhang, G., Zhang, J., Gao, Y., Li, Y., & Li, Y. (2021) · Expert Opinion on Drug Discovery · doi:10.1080/17460441.2021.1969359 · Cited by 102 · see citing works

Allosteric modulation of AURKA kinase activity by a small-molecule inhibitor of its protein-protein interaction with TPX2

Janecek, M., Rossmann, M., Sharma, P., Emery, A., Huggins, D. J., Stockwell, S. R., Stokes, J. E., Tan, Y. S., Guarino, E., Hardwick, B. S., et al. (2016) · Scientific Reports · doi:10.1038/srep28528 · Cited by 95 · see citing works

The natural product eugenol is an inhibitor of the ebola virus in vitro

Lane, T., Anantpadma, M., Freundlich, J. S., Davey, R. A., Madrid, P. B., & Ekins, S. (2019) · Pharmaceutical Research · doi:10.1007/s11095-019-2629-0 · Cited by 88 · see citing works

Condensation-Driven Assembly of Boron-Containing Bis(Heteroaryl) Motifs Using a Linchpin Approach

Adachi, S., Liew, S. K., Lee, C. F., Lough, A. J., He, Z., Denis, J. D. S., Poda, G. I., & Yudin, A. K. (2015) · Organic Letters · doi:10.1021/acs.orglett.5b02741 · Cited by 87 · see citing works

Drugging challenging targets using fragment-based approaches

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Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase

Landon, M. R., Lieberman, R. L., Hoang, Q. Q., Ju, S., Caaveiro, J. M. M., Orwig, S. D., Kozakov, D., Brenke, R., Chuang, G., Beglov, D., et al. (2009) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-009-9283-2 · Cited by 84 · see citing works

Fragment Informatics and Computational Fragment‐Based Drug Design: An Overview and Update

Sheng, C., & Zhang, W. (2013) · Medicinal Research Reviews · doi:10.1002/med.21255 · Cited by 80 · see citing works

N-Myristoyltransferase as a potential drug target in malaria and leishmaniasis

Tate, E. W., Bell, A., Rackham, M. D., & Wright, M. H. (2013) · Parasitology · doi:10.1017/s0031182013000450 · Cited by 77 · see citing works

Azetidine and Piperidine Carbamates as Efficient, Covalent Inhibitors of Monoacylglycerol Lipase

Butler, C. R., Beck, E. M., Harris, A. R., Huang, Z., McAllister, L. A., Ende, C. W. A., Fennell, K. F., Foley, T. L., Fonseca, K. R., Hawrylik, S. J., et al. (2017) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.7b01531 · Cited by 76 · see citing works

Assessment of Dengue virus helicase and methyltransferase as targets for fragment-based drug discovery

Coutard, B., Decroly, É., Li, C., Sharff, A., Lescar, J., Bricogne, G., & Barral, K. (2014) · Antiviral Research · doi:10.1016/j.antiviral.2014.03.013 · Cited by 73 · see citing works

Identification of ligand efficient, fragment-like hits from an HTS library: structure-based virtual screening and docking investigations of 2H- and 3H-pyrazolo tautomers for Aurora kinase A selectivity

Sarvagalla, S., Singh, V. K., Ke, Y., Shiao, H., Lin, W., Hsieh, H., Hsu, J. T.-A., & Coumar, M. S. (2014) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-014-9807-2 · Cited by 64 · see citing works

Antagonism of a zinc metalloprotease using a unique metal-chelating scaffold: tropolones as inhibitors of P. aeruginosa elastase

Fullagar, J. L., Garner, A. L., Struss, A. K., Day, J. A., Martin, D. P., Yu, J., Cai, X., Janda, K. D., & Cohen, S. M. (2013) · Chemical Communications · doi:10.1039/c3cc41191e · Cited by 64 · see citing works

AEG-1/MTDH/LYRIC in Liver Cancer

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Screening and hit evaluation of a chemical library against blood-stage Plasmodium falciparum

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Application of NMR and Molecular Docking in Structure-Based Drug Discovery

Stark, J. L., & Powers, R. (2011) · Topics in current chemistry · doi:10.1007/128_2011_213 · Cited by 59 · see citing works

Combining NMR and X-ray Crystallography in Fragment-Based Drug Discovery: Discovery of Highly Potent and Selective BACE-1 Inhibitors

Wyss, D. F., Wang, Y., Eaton, H. L., Strickland, C., Voigt, J. H., Zhu, Z., & Stamford, A. W. (2011) · Topics in current chemistry · doi:10.1007/128_2011_183 · Cited by 56 · see citing works

New developments in non-quinolone-based antibiotics for the inhibiton of bacterial gyrase and topoisomerase IV

Badshah, S. L., & Ullah, A. (2018) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2018.04.059 · Cited by 52 · see citing works

Docking and Linking of Fragments To Discover Jumonji Histone Demethylase Inhibitors

Korczynska, M., Le, D. D., Younger, N. S., Gregori‐Puigjané, E., Tumber, A., Krojer, T. J., Velupillai, S., Gileadi, C., Nowak, R. P., Iwasa, E., et al. (2015) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.5b01527 · Cited by 51 · see citing works

Discovery of Potent, Reversible, and Competitive Cruzain Inhibitors with Trypanocidal Activity: A Structure-Based Drug Design Approach

de Souza, M. L., Júnior, C. D. O. R., Ferreira, R. S., Espinoza-Chávez, R. M., Ferreira, L. L. G., Slafer, B. W., Magalhães, L. G., Krogh, R., Oliva, G., Cruz, F. C., et al. (2019) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.9b00802 · Cited by 50 · see citing works

Benzimidazole Inhibitors Induce a DFG-Out Conformation of Never in Mitosis Gene A-Related Kinase 2 (Nek2) without Binding to the Back Pocket and Reveal a Nonlinear Structure−Activity Relationship

Solanki, S., Innocenti, P., Mas-Droux, C., Boxall, K. J., Barillari, C., van Montfort, R. L. M., Aherne, G. W., Bayliss, R. W., & Hoelder, S. (2011) · Journal of Medicinal Chemistry · doi:10.1021/jm1011726 · Cited by 50 · see citing works

Optimization of a Fragment-Based Screening Hit toward Potent DOT1L Inhibitors Interacting in an Induced Binding Pocket

Scheufler, C., Möbitz, H., Gaul, C., Ragot, C., Be, C., Fernández, C. F., Beyer, K. S., Tiedt, R., & Stauffer, F. (2016) · ACS Medicinal Chemistry Letters · doi:10.1021/acsmedchemlett.6b00168 · Cited by 49 · see citing works

Potent and Selective Inhibitors of CK2 Kinase Identified through Structure-Guided Hybridization

Dowling, J. E., Chuaqui, C. E., Pontz, T. W., Lyne, P. D., Larsen, N., Block, M. H., Chen, H., Su, N., Wu, A. J., Russell, D. J., et al. (2012) · ACS Medicinal Chemistry Letters · doi:10.1021/ml200257n · Cited by 48 · see citing works

SPAM: A Simple Approach for Profiling Bound Water Molecules

Cui, G., Swails, J., & Manas, E. S. (2013) · Journal of Chemical Theory and Computation · doi:10.1021/ct400711g · Cited by 48 · see citing works

Fragment-Based Discovery of Indole Inhibitors of Matrix Metalloproteinase-13

Taylor, S. J., Abeywardane, A., Liang, S., Muegge, I., Padyana, A. K., Xiong, Z., Hill-Drzewi, M., Farmer, B. T., Li, X., Collins, B., et al. (2011) · Journal of Medicinal Chemistry · doi:10.1021/jm201129m · Cited by 47 · see citing works

Fragment-based screening by X-ray crystallography, MS and isothermal titration calorimetry to identify PNMT (phenylethanolamine N-methyltransferase) inhibitors

Drinkwater, N., Vu, H., Lovell, K. M., Criscione, K. R., Collins, B. M., Prisinzano, T. E., Poulsen, S., McLeish, M. J., Grunewald, G. L., & Martin, J. L. (2010) · Biochemical Journal · doi:10.1042/bj20100651 · Cited by 45 · see citing works

The Purchasable Chemical Space: A Detailed Picture

Lucas, X., Grüning, B. A., Bleher, S., & Günther, S. (2015) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5b00116 · Cited by 45 · see citing works

Optimization of Ligand and Lipophilic Efficiency To Identify an in Vivo Active Furano-Pyrimidine Aurora Kinase Inhibitor

Shiao, H., Coumar, M. S., Chun-Wei, C., Ke, Y., Chi, Y., Chu, C., Sun, H.-Y., Chen, C.-H., Lin, W., Fung, K.-S., et al. (2013) · Journal of Medicinal Chemistry · doi:10.1021/jm4006059 · Cited by 44 · see citing works

Molecular Property Filters Describing Pharmacokinetics and Drug Binding

García‐Sosa, A. T., Maran, U., & Hetényi, C. (2012) · Current Medicinal Chemistry · doi:10.2174/092986712799945021 · Cited by 44 · see citing works

Tuning the serum persistence of human serum albumin domain III:diabody fusion proteins

Kenanova, V. E., Olafsen, T., Salazar, F. B., Williams, L. E., Knowles, S. M., & Wu, A. M. (2010) · Protein Engineering Design and Selection · doi:10.1093/protein/gzq054 · Cited by 43 · see citing works

Electron Density Guided Fragment-Based Lead Discovery of Ketohexokinase Inhibitors

Gibbs, A. C., Abad, M. C., Zhang, X., Tounge, B. A., Lewandowski, F. A., Struble, G. T., Sun, W., Sui, Z., & Kuo, L. C. (2010) · Journal of Medicinal Chemistry · doi:10.1021/jm100677s · Cited by 41 · see citing works

In Vivo Evaluation of Selective Carbonic Anhydrase Inhibitors as Potential Anticonvulsant Agents

Bruno, E., Buemi, M. R., Luca, L. D., Ferro, S., Monforte, A., Supuran, C. T., Vullo, D., Sarro, G. D., Russo, E., & Gitto, R. (2016) · ChemMedChem · doi:10.1002/cmdc.201500596 · Cited by 39 · see citing works

Convergent 18 F radiosynthesis: A new dimension for radiolabelling

Li, L., Hopkinson, M. N., Yona, R. L., Béjot, R., Gee, A. D., & Gouverneur, V. (2010) · Chemical Science · doi:10.1039/c0sc00362j · Cited by 38 · see citing works

Discovery of small molecules targeting the tandem tudor domain of the epigenetic factor UHRF1 using fragment-based ligand discovery

Chang, L., Campbell, J. C., Raji, I. O., Guduru, S. K. R., Kandel, P., Nguyen, M., Liu, S., Tran, K., Venugopal, N. K., Taylor, B. C., et al. (2021) · Scientific Reports · doi:10.1038/s41598-020-80588-4 · Cited by 38 · see citing works

Efficiency of hit generation and structural characterization in fragment-based ligand discovery

Larsson, A., Jansson, A. E., Åberg, A., & Nordlund, P. (2011) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2011.06.008 · Cited by 36 · see citing works

Progress in discovery of small-molecule modulators of protein–protein interactions via fragment screening

Magee, T. V. (2015) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2015.04.089 · Cited by 34 · see citing works

Discovery of novel pyrrole-based scaffold as potent and orally bioavailable free fatty acid receptor 1 agonists for the treatment of type 2 diabetes

Li, Z., Pan, M., Su, X., Dai, Y., Fu, M., Cai, X., Shi, W., Huang, W., & Qian, H. (2016) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2016.03.014 · Cited by 34 · see citing works

Proteome‐Wide Fragment‐Based Ligand and Target Discovery

Forrest, I., & Parker, C. G. (2023) · Israel Journal of Chemistry · doi:10.1002/ijch.202200098 · Cited by 30 · see citing works

Pharmacophore modeling and its applications

Tyagi, R., Singh, A., Chaudhary, K. K., & Yadav, M. K. (2021) · Elsevier eBooks · doi:10.1016/b978-0-323-89775-4.00009-2 · Cited by 36 · see citing works

Rational Design Strategies in DNA‐Encoded Libraries for Drug Discovery

Wang, X., Li, L., Shen, X., & Lu, X. (2025) · Angewandte Chemie International Edition · doi:10.1002/anie.202511839 · Cited by 29 · see citing works

Advances in fragment-based drug discovery platforms

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Aminoindazole PDK1 Inhibitors: A Case Study in Fragment-Based Drug Discovery

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Discovery of Novel Pneumococcal Surface Antigen A (PsaA) Inhibitors Using a Fragment-based Drug Design Approach

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