<!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"
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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-6891</article-id>
      <article-id pub-id-type="doi">10.51847/x5pK88lN9y</article-id>
      <article-categories>
        <subj-group subj-group-type="heading">
          <subject>Original research</subject>
        </subj-group>
      </article-categories>
      <title-group>
        <article-title>Diffusion Models for Macrocyclic Peptide Design Using Stability, Permeability, and Binding Constraints</article-title>
      </title-group>
                    <contrib-group>
                      <contrib contrib-type="author">
              <name>
                <surname>O’Connor</surname>
                <given-names>Patrick</given-names>
              </name>
                              <xref rid="aff1" ref-type="aff">1</xref>
                                                            <xref rid="cor1" ref-type="corresp" />
                          </contrib>
                      <contrib contrib-type="author">
              <name>
                <surname>Murphy</surname>
                <given-names>Sean</given-names>
              </name>
                              <xref rid="aff1" ref-type="aff">1</xref>
                                        </contrib>
                  </contrib-group>
                  <aff id="aff1">
            <label>1</label>Department of Pharmaceutical Informatics and Analytics, Faculty of Pharmacy, Trinity College Dublin, Dublin, Ireland.
          </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="patrick.oconnor@gmail.com">patrick.oconnor@gmail.com</email>
                          </corresp>
          </author-notes>
                    <pub-date pub-type="epub">
        <day>28</day>
        <month>04</month>
        <year>2026</year>
      </pub-date>
      <volume>17</volume>
      <issue>2</issue>
      <fpage>54</fpage>
      <lpage>62</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>Macrocyclic peptides can address challenging therapeutic targets that are often poorly modulated by conventional small molecules or biologics, but their design is difficult because conformational preorganization, membrane permeability, and target binding are interdependent and sometimes competing requirements. Existing generative approaches for peptides often focus on sequence novelty or target affinity without fully accounting for the geometric constraints imposed by cyclization, highlighting the need for models that reason jointly over topology, conformation, and medicinal chemistry properties. This article proposes a diffusion-based generative framework for designing macrocyclic peptides conditioned on predicted conformational stability, membrane permeability, and binding affinity, enabling the generation of candidate macrocycles that satisfy multiple design criteria within a single generative process. The model operates on cyclization-aware three-dimensional coordinates or torsion-angle representations, with property predictors guiding denoising toward molecular structures that exhibit favorable therapeutic profiles. Conceptually, this approach can produce synthetically plausible macrocyclic peptides with desirable permeability, target engagement, and conformational preferences, which should then be evaluated through computational filters, molecular dynamics simulations, and prospective experimental testing before being considered as drug leads. By integrating structural generation with pharmacokinetic and pharmacodynamic constraints, multi-constraint diffusion generation offers a model-oriented strategy for efficiently exploring drug-like macrocyclic peptide chemical space and accelerating the rational design of constrained peptide therapeutics.</p>
      </abstract>
      <kwd-group>
                <kwd>Diffusion models</kwd>
                <kwd>Macrocyclic peptides</kwd>
                <kwd>Peptide therapeutics</kwd>
                <kwd>Molecular generation</kwd>
                <kwd>Permeability</kwd>
                <kwd>Conformational stability</kwd>
              </kwd-group>
    </article-meta>
  </front>
</article>