Hit to lead

<h2 id="hit-confirmation">Hit confirmation</h2>
<p>After hits are identified from a high throughput screen, the hits are confirmed and evaluated using the following methods:
</p>
<ul><li>Confirmatory testing: compounds that were found active against the selected target are re-tested using the same assay conditions used during the HTS to make sure that the activity is reproducible.</li>
<li>Dose response curve: the compound is tested over a range of concentrations to determine the concentration that results in half maximal binding or activity (<a href="/facts/IC50/zdz6qVBP">IC50</a> or <a href="/facts/EC50/x7oD7ITx">EC50</a> value respectively).</li>
<li>Orthogonal testing: confirmed hits are assayed using a different assay which is usually closer to the target physiological condition or using a different technology.</li>
<li>Secondary screening: confirmed hits are tested in a functional cellular assay to determine <a href="/facts/Intrinsic_activity/wRugal9r">efficacy</a>.</li>
<li>Synthetic tractability: medicinal chemists evaluate compounds according to their synthesis feasibility and other parameters such as up-scaling or cost of goods.</li>
<li>Biophysical testing: <a href="/facts/Nuclear_magnetic_resonance/pGYAn9Bz">nuclear magnetic resonance</a> (NMR), <a href="/facts/Isothermal_titration_calorimetry/f66oUR3u">isothermal titration calorimetry</a> (ITC), <a href="/facts/Dynamic_light_scattering/dAJRM90w">dynamic light scattering</a> (DLS), <a href="/facts/Surface_plasmon_resonance/8JKldMUT">surface plasmon resonance</a> (SPR), <a href="/facts/Dual_polarisation_interferometry/opICunH9">dual polarisation interferometry</a> (DPI), <a href="/facts/Microscale_thermophoresis/twyUpIHj">microscale thermophoresis</a> (MST) are commonly used to assess whether the compound binds effectively to the target, the <a href="/facts/Receptor%E2%80%93ligand_kinetics/DrJVaGrg">kinetics</a>, <a href="/facts/Thermodynamics/q4hIx3yP">thermodynamics</a>, and <a href="/facts/Stoichiometry/I5p9cJzV">stoichiometry</a> of binding, any associated <a href="/facts/Conformational_change/q23CgKgo">conformational change</a> and to rule out promiscuous binding.</li>
<li>Hit ranking and clustering: Confirmed hit compounds are then ranked according to the various hit confirmation experiments.</li>
<li><a href="/facts/Freedom_to_operate/7vH9JvMF">Freedom to operate</a> evaluation: hit structures are checked in specialized databases to determine if they are patentable.<a class="footnote-ref" id="fnref:6" href="#fn:6"><sup>6</sup></a></li></ul>
<h2 id="hit-expansion">Hit expansion</h2>
<p>Following hit confirmation, several compound clusters will be chosen according to their characteristics in the previously defined tests. An Ideal compound cluster will contain members that possess:
</p>
<ul><li>high <a href="/facts/Binding_affinity/44QLL4eU">affinity</a> towards the target (less than 1 μM)</li>
<li><a href="/facts/Binding_selectivity/RryTsdGv">selectivity</a> versus other targets</li>
<li>significant <a href="/facts/Intrinsic_activity/wRugal9r">efficacy</a> in a cellular assay</li>
<li><a href="/facts/Druglikeness/ATGG3HHI">druglikeness</a> (moderate molecular weight and <a href="/facts/Lipophilicity/AWpsR8Xe">lipophilicity</a> usually estimated as <a href="/facts/Partition_coefficient/D4aTlBal">ClogP</a>). Affinity, molecular weight and lipophilicity can be linked in single parameter such as <a href="/facts/Ligand_efficiency/M95e7RBE">ligand efficiency</a> and <a href="/facts/Lipophilic_efficiency/vSrLu60J">lipophilic efficiency</a>.</li>
<li>low to moderate binding to human <a href="/facts/Serum_albumin/KW1YhuF3">serum albumin</a></li>
<li>low interference with <a href="/facts/P450/alxusFD0">P450</a> enzymes and <a href="/facts/P-glycoprotein/RY6qLKjq">P-glycoproteins</a></li>
<li>low <a href="/facts/Cytotoxicity/SQuTTLoL">cytotoxicity</a></li>
<li>metabolic stability</li>
<li>high cell membrane permeability</li>
<li>sufficient water solubility (above 10 μM)</li>
<li>chemical stability</li>
<li>synthetic tractability</li>
<li>patentability</li></ul>
<p>The project team will usually select between three and six compound series to be further explored. The next step will allow the testing of analogous compounds to determine a <a href="/facts/Quantitative_structure-activity_relationship/6RDyCQDD">quantitative structure-activity relationship</a> (QSAR). Analogs can be quickly selected from an internal library or purchased from commercially available sources ("SAR by catalog" or "SAR by purchase"). Medicinal chemists will also start synthesizing related compounds using different methods such as <a href="/facts/Combinatorial_chemistry/WW2SSJnq">combinatorial chemistry</a>, high-throughput chemistry, or more classical <a href="/facts/Organic_chemistry/djxhxaNg">organic chemistry</a> synthesis.
</p>
<h2 id="lead-optimization-phase">Lead optimization phase</h2>
<p>The objective of this drug discovery phase is to synthesize <a href="/facts/Lead_compound/5wFoEqmS">lead compounds</a>, new analogs with improved potency, reduced off-target activities, and physiochemical/metabolic properties suggestive of reasonable <i>in vivo</i> <a href="/facts/Pharmacokinetics/x4CUUnle">pharmacokinetics</a>.<a class="footnote-ref" id="fnref:7" href="#fn:7"><sup>7</sup></a><a class="footnote-ref" id="fnref:8" href="#fn:8"><sup>8</sup></a> This optimization is accomplished through chemical modification of the hit structure, with modifications chosen by employing knowledge of the <a href="/facts/Structure%E2%80%93activity_relationship/S2RxpCUK">structure–activity relationship</a> (SAR) as well as structure-based design if structural information about the target is available.
</p><p>Lead optimization is concerned with experimental testing and confirmation of the compound based on animal efficacy models and <a href="/facts/ADME-Tox/fPpj3sEW">ADMET</a> (<i>in vitro</i> and <i>in situ</i>) tools that may be followed by target identification and target validation.
</p>
<h2 id="best-practices-for-hit-finding">Best Practices for Hit Finding</h2>
<p>For educational purposes the European Federation for Medicinal Chemistry and Chemical Biology (EFMC) shared a series of webinars including 'Best Practices for Hit Finding' as well as 'Hit Generation Case Studies'.<a class="footnote-ref" id="fnref:9" href="#fn:9"><sup>9</sup></a>
</p>
<h2 id="see-also">See also</h2>

<ul><li><a href="/facts/Cheminformatics/BwBkT11c">Cheminformatics</a></li>
<li><a href="/facts/Drug_design/XAU0Ke3d">Drug design</a></li>
<li><a href="/facts/Drug_development/k34jgV4B">Drug development</a></li>
<li><a href="/facts/Drug_metabolism/I5nQ28Ma">Drug metabolism</a></li>
<li><a href="/facts/Fragment-based_lead_discovery/HIcPT4Pz">Fragment-based lead discovery</a> (FBLD)</li>
<li><a href="/facts/High-content_screening/HGb9JEoj">High-content screening</a> (HCS)</li>
<li><a href="/facts/High-throughput_screening/503vkz1b">High-throughput screening</a> (HTS)</li>
<li><a href="/facts/Pharmaceutical_company/5mCITYys">Pharmaceutical company</a></li>
<li><a href="/facts/Rational_drug_design/XAU0Ke3d">Rational drug design</a></li></ul>

<h2 id="references">References</h2>

<ol>
<li id="fn:1"><p>Deprez-Poulain R, Deprez B (2004). "Facts, figures and trends in lead generation". Current Topics in Medicinal Chemistry. 4 (6): 569–80. doi:10.2174/1568026043451168. PMID 14965294. <a href="/wiki/Doi_(identifier)" target="_blank">/wiki/Doi_(identifier)</a> <a href="#fnref:1" class="footnote-back-ref">↩</a></p></li>
<li id="fn:2"><p>Fruber M, Narjes F, Steele J (2013). "Lead Generation". In Davis A, Ward SE (eds.). Handbook of Medicinal Chemistry: Principles and Practice. RSC Books. pp. 505–528. ISBN 978-1849736251. <a href="978-1849736251" target="_blank">978-1849736251</a> <a href="#fnref:2" class="footnote-back-ref">↩</a></p></li>
<li id="fn:3"><p>Keseru GM, Makara GM (Aug 2006). "Hit discovery and hit-to-lead approaches". Drug Discovery Today. 11 (15–16): 741–8. doi:10.1016/j.drudis.2006.06.016. PMID 16846802. <a href="/wiki/Doi_(identifier)" target="_blank">/wiki/Doi_(identifier)</a> <a href="#fnref:3" class="footnote-back-ref">↩</a></p></li>
<li id="fn:4"><p>Bleicher KH, Böhm HJ, Müller K, Alanine AI (May 2003). "Hit and lead generation: beyond high-throughput screening". Nature Reviews. Drug Discovery. 2 (5): 369–78. doi:10.1038/nrd1086. PMID 12750740. S2CID 4859609. <a href="/wiki/Doi_(identifier)" target="_blank">/wiki/Doi_(identifier)</a> <a href="#fnref:4" class="footnote-back-ref">↩</a></p></li>
<li id="fn:5"><p>Ezekiel J. Emanuel. "The Solution to Drug Prices". New York Times. On average, only one in every 5,000 compounds that drug companies discover and put through preclinical testing becomes an approved drug. Of the drugs started in clinical trials on humans, only 10 percent secure F.D.A. approval. ... <a href="/wiki/Ezekiel_J._Emanuel" target="_blank">/wiki/Ezekiel_J._Emanuel</a> <a href="#fnref:5" class="footnote-back-ref">↩</a></p></li>
<li id="fn:6"><p>Cockbain J (2007). "Intellectual property rights and patents". In Triggle JB, Taylor DJ (ed.). Comprehensive Medicinal Chemistry. Vol. 1 (2nd ed.). Amsterdam: Elsevier. pp. 779–815. doi:10.1016/B0-08-045044-X/00031-6. ISBN 978-0-08-045044-5. <a href="978-0-08-045044-5" target="_blank">978-0-08-045044-5</a> <a href="#fnref:6" class="footnote-back-ref">↩</a></p></li>
<li id="fn:7"><p>Beckers, Maximilian; Fechner, Nikolas; Stiefl, Nikolaus (2022-12-12). "25 Years of Small-Molecule Optimization at Novartis: A Retrospective Analysis of Chemical Series Evolution". Journal of Chemical Information and Modeling. 62 (23): 6002–6021. doi:10.1021/acs.jcim.2c00785. ISSN 1549-9596. <a href="https://pubs.acs.org/doi/10.1021/acs.jcim.2c00785" target="_blank">https://pubs.acs.org/doi/10.1021/acs.jcim.2c00785</a> <a href="#fnref:7" class="footnote-back-ref">↩</a></p></li>
<li id="fn:8"><p>Brown, Dean G. (2023-06-08). "An Analysis of Successful Hit-to-Clinical Candidate Pairs". Journal of Medicinal Chemistry. 66 (11): 7101–7139. doi:10.1021/acs.jmedchem.3c00521. ISSN 0022-2623. <a href="https://pubs.acs.org/doi/abs/10.1021/acs.jmedchem.3c00521" target="_blank">https://pubs.acs.org/doi/abs/10.1021/acs.jmedchem.3c00521</a> <a href="#fnref:8" class="footnote-back-ref">↩</a></p></li>
<li id="fn:9"><p>"Hit Generation". <a href="https://www.efmc.info/hit-generation" target="_blank">https://www.efmc.info/hit-generation</a> <a href="#fnref:9" class="footnote-back-ref">↩</a></p></li>
</ol>

Hit to lead open-in-new

Hit to lead