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  <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-6973</article-id>
      <article-id pub-id-type="doi">10.51847/xskHpKqRO2</article-id>
      <article-categories>
        <subj-group subj-group-type="heading">
          <subject>Original research</subject>
        </subj-group>
      </article-categories>
      <title-group>
        <article-title>Binding Affinity Is Not Binding Behavior: Reframing Learned Molecular Recognition around Kinetics, Conformational Change, and Residence Time</article-title>
      </title-group>
                    <contrib-group>
                      <contrib contrib-type="author">
              <name>
                <surname>Jallow</surname>
                <given-names>Binta</given-names>
              </name>
                              <xref rid="aff1" ref-type="aff">1</xref>
                                                            <xref rid="cor1" ref-type="corresp" />
                          </contrib>
                      <contrib contrib-type="author">
              <name>
                <surname>Conteh</surname>
                <given-names>Musa</given-names>
              </name>
                              <xref rid="aff2" ref-type="aff">2</xref>
                                        </contrib>
                      <contrib contrib-type="author">
              <name>
                <surname>Okafor</surname>
                <given-names>Christopher</given-names>
              </name>
                              <xref rid="aff3" ref-type="aff">3</xref>
                                        </contrib>
                      <contrib contrib-type="author">
              <name>
                <surname>Sanyang</surname>
                <given-names>Fatou</given-names>
              </name>
                              <xref rid="aff4" ref-type="aff">4</xref>
                                        </contrib>
                  </contrib-group>
                  <aff id="aff1">
            <label>1</label>Department of Molecular Recognition and Binding Kinetics, Faculty of Pharmacy, University of Gambia, Banjul, Gambia.
          </aff>
                  <aff id="aff2">
            <label>2</label>Department of Conformational Change and Binding Behavior, Faculty of Pharmacy, University of Sierra Leone, Freetown, Sierra Leone.
          </aff>
                  <aff id="aff3">
            <label>3</label>Department of Residence Time and Drug-Target Engagement, Faculty of Pharmaceutical Sciences, University of Nigeria, Nsukka, Nigeria.
          </aff>
                  <aff id="aff4">
            <label>4</label>Department of Kinetics-Driven Molecular Recognition, Faculty of Pharmacy, University of Cape Town, Cape Town, South Africa.
          </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="binta.jallow@utg.edu.gm">binta.jallow@utg.edu.gm</email>
                          </corresp>
          </author-notes>
                    <pub-date pub-type="epub">
        <day>28</day>
        <month>02</month>
        <year>2025</year>
      </pub-date>
      <volume>16</volume>
      <issue>1</issue>
      <fpage>81</fpage>
      <lpage>90</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>Equilibrium affinity remains a central descriptor of molecular recognition, yet it cannot by itself explain how rapidly a ligand reaches its target, which conformational states enable binding, how the complex reorganizes after encounter, which pathways control dissociation, or how long target engagement persists under changing biological conditions. This limitation is increasingly consequential for computational pharmaceutical science because models trained primarily on affinity labels may learn endpoint compatibility while overlooking the temporal and conformational behavior that connects molecular structure to pharmacological action. This Original Molecular-Modeling Perspective Article develops a proposed reframing of learned molecular recognition around a Dynamic Recognition Profile. The profile retains equilibrium affinity as one evidentiary component while separately representing conformational ensembles, recognition mechanisms, association and dissociation pathways, kinetic rate parameters, residence time, perturbation responses, pharmacological context, uncertainty, and provenance. The synthesis distinguishes conformational selection from induced fit without treating them as mutually exclusive, separates thermodynamic stability from kinetic barriers, and argues that trajectory, assay, structural, and perturbational evidence should remain distinguishable when incorporated into learned models. It further proposes that evaluation should move beyond one predictive error measure toward tests of ensemble fidelity, pathway reproducibility, kinetic calibration, perturbation sensitivity, transfer across chemical and target domains, and bounded decision usefulness. The contribution is conceptual rather than empirically validated. It does not establish that kinetic optimization is universally advantageous, that simulated pathways are mechanistically definitive, or that residence time alone determines efficacy, selectivity, or dosing. Reframing recognition as conditional behavior may nevertheless support more scientifically interpretable models and more disciplined translation from molecular prediction to pharmaceutical reasoning.</p>
      </abstract>
      <kwd-group>
                <kwd>Binding kinetics</kwd>
                <kwd>Molecular recognition</kwd>
                <kwd>Residence time</kwd>
                <kwd>Conformational selection</kwd>
                <kwd>Induced fit</kwd>
                <kwd>Unbinding pathways</kwd>
              </kwd-group>
    </article-meta>
  </front>
</article>