<!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD with MathML3 v1.3 20210610//EN" "JATS-archivearticle1-3-mathml3.dtd"><article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"
  dtd-version="1.3" xml:lang="en" article-type="research-article">
  <?DTDIdentifier.IdentifierValue -//NLM//DTD JATS (Z39.96) Journal Publishing DTD v1.2 20190208//EN?>
  <?DTDIdentifier.IdentifierType public?>
  <?SourceDTD.DTDName JATS-journalpublishing1.dtd?>
  <?SourceDTD.Version 1.2?>
  <?ConverterInfo.XSLTName jats2jats3.xsl?>
  <?ConverterInfo.Version 1?>
  <?properties open_access?>
  <front>
    <journal-meta>
      <journal-id journal-id-type="iso-abbrev">Pharmacophore</journal-id>
      <journal-id journal-id-type="publisher-id">pharmacophorejournal.com</journal-id>
      <journal-id journal-id-type="publisher-id">Pharmacophore</journal-id>
      <journal-title-group>
        <journal-title>Pharmacophore</journal-title>
      </journal-title-group>
      <issn pub-type="epub">2229-5402</issn>
    </journal-meta>
    <article-meta>
      <article-id pub-id-type="publisher-id">pharmacophorejournal.com-6983</article-id>
      <article-id pub-id-type="doi">10.51847/rSRfIoYpgX</article-id>
      <article-categories>
        <subj-group subj-group-type="heading">
          <subject>Original research</subject>
        </subj-group>
      </article-categories>
      <title-group>
        <article-title>From Predicted Binding to Defensible Candidate Advancement: A Conceptual Framework for Integrating Mechanistic Plausibility, Translational Uncertainty, and Decision Thresholds in Artificial Intelligence–Driven Drug Discovery</article-title>
      </title-group>
                    <contrib-group>
                      <contrib contrib-type="author">
              <name>
                <surname>Petrova</surname>
                <given-names>Elena</given-names>
              </name>
                              <xref rid="aff1" ref-type="aff">1</xref>
                                        </contrib>
                      <contrib contrib-type="author">
              <name>
                <surname>Weber</surname>
                <given-names>Marcus</given-names>
              </name>
                              <xref rid="aff2" ref-type="aff">2</xref>
                                                            <xref rid="cor1" ref-type="corresp" />
                          </contrib>
                      <contrib contrib-type="author">
              <name>
                <surname>Nair</surname>
                <given-names>Priya</given-names>
              </name>
                              <xref rid="aff3" ref-type="aff">3</xref>
                                        </contrib>
                      <contrib contrib-type="author">
              <name>
                <surname>Andersen</surname>
                <given-names>Thomas</given-names>
              </name>
                              <xref rid="aff4" ref-type="aff">4</xref>
                                        </contrib>
                  </contrib-group>
                  <aff id="aff1">
            <label>1</label>Department of AI-Driven Drug Discovery, Faculty of Pharmacy, Sofia University, Sofia, Bulgaria.
          </aff>
                  <aff id="aff2">
            <label>2</label>Department of Computational Pharmacology and Molecular Informatics, Faculty of Medicine, LMU Munich, Munich, Germany.
          </aff>
                  <aff id="aff3">
            <label>3</label>Department of Pharmaceutical Data Science and Cheminformatics, Indian Institute of Technology Bombay, Mumbai, India.
          </aff>
                  <aff id="aff4">
            <label>4</label>Department of Drug Design and Translational Pharmacology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
          </aff>
                          <author-notes>
            <corresp id="cor1">
              <bold>Address for correspondence:</bold> Prof. Wael Abu Dayyih, Department of
              Pharmaceutical Chemistry, Faculty of Pharmacy, Mutah University, Al-Karak 61710, Jordan.
                              E-mail: <email xlink:href="marcus.weber@lmu.de">marcus.weber@lmu.de</email>
                          </corresp>
          </author-notes>
                    <pub-date pub-type="epub">
        <day>28</day>
        <month>10</month>
        <year>2026</year>
      </pub-date>
      <volume>17</volume>
      <issue>5</issue>
      <fpage>9</fpage>
      <lpage>16</lpage>
      <permissions>
        <copyright-statement>
          Copyright: &#x000a9; 2026 Pharmacophore
        </copyright-statement>
        <copyright-year>2026</copyright-year>
        <license>
          <ali:license_ref xmlns:ali="http://www.niso.org/schemas/ali/1.0/"
            specific-use="textmining" content-type="ccbyncsalicense">
            https://creativecommons.org/licenses/by-nc-sa/4.0/</ali:license_ref>
          <license-p>This is an open access journal, and articles are distributed under the terms of
            the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 License, which allows
            others to remix, tweak, and build upon the work non-commercially, as long as appropriate
            credit is given and the new creations are licensed under the identical terms.</license-p>
        </license>
      </permissions>
      <abstract>
        <title>A<sc>BSTRACT</sc></title>
        <p>Artificial intelligence increasingly supports molecular generation, structural prediction, affinity estimation and property prediction in drug discovery, yet a favorable computational score does not itself establish that a candidate should advance. The central problem is therefore not whether AI can predict binding or related molecular properties, but how such predictions should be interpreted alongside mechanistic plausibility, translational evidence, uncertainty and the consequences of an advancement decision. This conceptual article develops an evidence-bounded candidate-advancement account that separates prediction quality from candidate-worthiness. It first identifies the justificatory limits of prediction-centred selection, including state dependence, benchmark leakage, out-of-distribution failure, calibration limitations and the conditional relevance of biological data. It then examines evidence that can strengthen or weaken an advancement case, including target engagement, pharmacological characterization, target assessment, orthogonal experimental confirmation and human translation. The resulting argument treats evidence layers as heterogeneous rather than automatically commensurable and proposes that uncertainty changes the burden of evidence required for progression Favorable AI predictions can therefore remain insufficient when mechanistic incoherence, unresolved distribution shift, weak target biology or adverse translational evidence persists. Conversely, a candidate can become more defensible as distinct uncertainties are retired through evidence appropriate to their level. Candidate advancement should thus be framed as a state-dependent decision under uncertainty, not as the maximization of a single predictive score.</p>
      </abstract>
      <kwd-group>
                <kwd>AI-driven drug discovery</kwd>
                <kwd>Candidate advancement</kwd>
                <kwd>Mechanistic plausibility</kwd>
                <kwd>Translational evidence</kwd>
                <kwd>Uncertainty calibration</kwd>
                <kwd>Predictive validity</kwd>
              </kwd-group>
    </article-meta>
  </front>
</article>
