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...
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 <...
Modeling gravitational instabilities in the partially molten crust with a Volume-Of-Fluid method
Modeling gravitational instabilities in the partially molten crust with a Volume-Of-Fluid method
<p><span>This work aims at </span><span>investigat</span><span>ing</span><s...
Cometary Physics Laboratory: spectrophotometric experiments
Cometary Physics Laboratory: spectrophotometric experiments
<p><strong><span dir="ltr" role="presentation">1. Introduction</span></strong&...

