Javascript must be enabled to continue!
<span class="word">Exploratory <span class="word allCaps">AI-<span class="word"><span class="changedDisabled">Assisted <span class="word allCaps">ML <span class="word"><span class="changedDisabled">Screening <s
View through CrossRef
This technical note reports an exploratory, AI-assisted in silico proof of concept implementing a “signaling first, killing later” discovery paradigm: prioritizing compounds with high predicted affinity for bacterial quorum sensing (QS) pathways, then refining them for bactericidal potency. Using Claude Opus 4.6 (Anthropic), a custom SMILES-based descriptor calculator (170+ features) and a four-model ensemble (Random Forest, Gradient Boosting, SVM-RBF, Logistic Regression) were trained on 150 compounds (87 QS modulators, 63 negatives), achieving cross-validated AUC of 0.954 ± 0.024. Screening 218 ZINC15 CEBB tranche compounds identified 101 Tier 1 hits (46.3%), of which 91.1% were nitroaromatic. Bioisosteric modifications rescued 9/15 analogs (60%) as PAINS-clean. An orthogonal antibiotic-likeness model (44 antibiotics vs. 49 non-antibiotics, AUC = 0.809) identified a diacetyl hexahydroxytriphenylene prodrug as dual-high (P_QS = 0.849, P_Abx = 0.876). Six iterative optimization cycles across two phases—structural alert reduction followed by scaffold simplification—produced the final lead M6-12 (SMILES: CNCc1c(F)cc(OC)c2c(OC)c3C(O)CNCC3c(O)c12), a partially saturated fluorinated piperidine-fused tricyclic scaffold. M6-12 achieved: dual-high ML convergence (P_QS = 0.928, P_Abx = 0.792, Joint = 0.735, 4/4 ABX models >0.5), zero PAINS, zero Brenk alerts, zero violations across all five drug-likeness filters, zero CYP inhibition (SwissADME 0/5, pkCSM 0/7), AMES-negative, high GI absorption, and “Very soluble” classification. RDKit validation confirmed: MW = 340.40, Crippen LogP = 0.48, TPSA = 82.98 Ų, HBD = 4, HBA = 6, Fraction Csp3 = 0.647. ChEMBL similarity: 0% at 95% threshold. Property-space MIC estimation: 2–32 μg/mL (Gram-positive), 1–11 μg/mL (Escherichia coli), 33–333 μg/mL (Pseudomonas aeruginosa), with 5/5 Richter rule compliance for Gram-negative penetration. A single pkCSM hepatotoxicity flag—contextualized by zero CYP inhibition, AMES-negative status, and low lipophilicity—probably constitutes the principal limitation requiring in vitro resolution. The signaling-first approach may enrich for molecules operating within biologically relevant chemical spaces, potentially offering a reduction in attrition compared to conventional MIC-first screening. All results require experimental validation.
Title: <span class="word">Exploratory <span class="word allCaps">AI-<span class="word"><span class="changedDisabled">Assisted <span class="word allCaps">ML <span class="word"><span class="changedDisabled">Screening <s
Description:
This technical note reports an exploratory, AI-assisted in silico proof of concept implementing a “signaling first, killing later” discovery paradigm: prioritizing compounds with high predicted affinity for bacterial quorum sensing (QS) pathways, then refining them for bactericidal potency.
Using Claude Opus 4.
6 (Anthropic), a custom SMILES-based descriptor calculator (170+ features) and a four-model ensemble (Random Forest, Gradient Boosting, SVM-RBF, Logistic Regression) were trained on 150 compounds (87 QS modulators, 63 negatives), achieving cross-validated AUC of 0.
954 ± 0.
024.
Screening 218 ZINC15 CEBB tranche compounds identified 101 Tier 1 hits (46.
3%), of which 91.
1% were nitroaromatic.
Bioisosteric modifications rescued 9/15 analogs (60%) as PAINS-clean.
An orthogonal antibiotic-likeness model (44 antibiotics vs.
49 non-antibiotics, AUC = 0.
809) identified a diacetyl hexahydroxytriphenylene prodrug as dual-high (P_QS = 0.
849, P_Abx = 0.
876).
Six iterative optimization cycles across two phases—structural alert reduction followed by scaffold simplification—produced the final lead M6-12 (SMILES: CNCc1c(F)cc(OC)c2c(OC)c3C(O)CNCC3c(O)c12), a partially saturated fluorinated piperidine-fused tricyclic scaffold.
M6-12 achieved: dual-high ML convergence (P_QS = 0.
928, P_Abx = 0.
792, Joint = 0.
735, 4/4 ABX models >0.
5), zero PAINS, zero Brenk alerts, zero violations across all five drug-likeness filters, zero CYP inhibition (SwissADME 0/5, pkCSM 0/7), AMES-negative, high GI absorption, and “Very soluble” classification.
RDKit validation confirmed: MW = 340.
40, Crippen LogP = 0.
48, TPSA = 82.
98 Ų, HBD = 4, HBA = 6, Fraction Csp3 = 0.
647.
ChEMBL similarity: 0% at 95% threshold.
Property-space MIC estimation: 2–32 μg/mL (Gram-positive), 1–11 μg/mL (Escherichia coli), 33–333 μg/mL (Pseudomonas aeruginosa), with 5/5 Richter rule compliance for Gram-negative penetration.
A single pkCSM hepatotoxicity flag—contextualized by zero CYP inhibition, AMES-negative status, and low lipophilicity—probably constitutes the principal limitation requiring in vitro resolution.
The signaling-first approach may enrich for molecules operating within biologically relevant chemical spaces, potentially offering a reduction in attrition compared to conventional MIC-first screening.
All results require experimental validation.
Related Results
On Flores Island, do "ape-men" still exist? https://www.sapiens.org/biology/flores-island-ape-men/
On Flores Island, do "ape-men" still exist? https://www.sapiens.org/biology/flores-island-ape-men/
<span style="font-size:11pt"><span style="background:#f9f9f4"><span style="line-height:normal"><span style="font-family:Calibri,sans-serif"><b><spa...
Crescimento de feijoeiro sob influência de carvão vegetal e esterco bovino
Crescimento de feijoeiro sob influência de carvão vegetal e esterco bovino
<p align="justify"><span style="color: #000000;"><span style="font-family: 'Times New Roman', serif;"><span><span lang="pt-BR">É indiscutível a import...
Automatic classification of paddy leaf disease
Automatic classification of paddy leaf disease
<span lang="EN-MY">Riceisastaple<span>f</span>o<span>o</span>din<span>m</span>ost<span>o</span>ft<span>h</span>e&l...
EDHAYA SUKOHARJO PEMADATAN OLEH M.TH. SRI MULYANI
EDHAYA SUKOHARJO PEMADATAN OLEH M.TH. SRI MULYANI
<p><span>Tari <span><em>Bedhaya Sukoharjo </em><span>garap padat merupakan bentuk tari <span><em>bedhaya </em><span>yang...
Hubungan Perilaku Pola Makan dengan Kejadian Anak Obesitas
Hubungan Perilaku Pola Makan dengan Kejadian Anak Obesitas
<p><em><span style="font-size: 11.0pt; font-family: 'Times New Roman',serif; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-langua...
Effects of a new land surface parametrization scheme on thermal extremes in a Regional Climate Model
Effects of a new land surface parametrization scheme on thermal extremes in a Regional Climate Model
<p><span>The </span><span>EFRE project Big Data@Geo aims at providing high resolution </span><span&...
Stress transfer process in doublet events studied by numerical TREMOL simulations: Study case Ometepec 1982 Doublet.
Stress transfer process in doublet events studied by numerical TREMOL simulations: Study case Ometepec 1982 Doublet.
<pre class="western"><span><span lang="en-US">Earthquake doublets are a characteristic rupture <...
Relationship Domain of Form Six Teachers Thinking in Teaching with External Factors of Form Six Teachers
Relationship Domain of Form Six Teachers Thinking in Teaching with External Factors of Form Six Teachers
<!--[if gte mso 9]><xml> <o:OfficeDocumentSettings> <o:RelyOnVML /> <o:AllowPNG /> </o:OfficeDocumentSettings> </xml><![endif]--> &l...

