What Small-Molecule Drug Screening got wrong, from 14 theses

Tried and failed

multi-kinase inhibitor drug screening validation applied to drug-resistant cancer cell lines. Outcome: no signal. Reason: candidate inhibitors failed to replicate increased inhibition during dose-response validation

Identifying Vulnerabilities and Novel Drug Candidates in Platinum-Resistant Ovarian Cancer. · Harvard · Master's

Tried and failed

high-throughput phenotypic screening for candidate target selection applied to therapeutic target validation in cancer cells. Outcome: did not generalise. Reason: top-scoring screening candidate failed to reproduce apoptotic or anti-proliferative effects in secondary validation assays

Modulation of miR-361-3p alters apoptosis in endocrine-resistant and -responsive breast cancer · Imperial · PhD

Tried and failed

molecular docking virtual screening compared to biophysical assays applied to fragment library screening against RNA targets. Outcome: no signal. Reason: computational docking hits showed zero overlap with surface plasmon resonance experimental binding hits

Can In-Silico Computational Virtual Screening of Fragment Libraries Model In-Vitro Biophysical Screening Methods with Similar Results to Identify Novel RNA-Binding Chemical Matter · Harvard · Master's

Tried and failed

structure-based virtual screening with flexible docking applied to bacterial beta-lactamase enzyme inhibition. Outcome: no signal. Reason: top docking-ranked small molecule hits failed to show enzymatic inhibition in vitro

Identifying Novel Inhibitors Against Klebsiella pneumoniae carbanepenamse-2 Enzymes Found in Carbapenem-Resistant Bacteria Through Structure-Based Small Molecule Virtual Screening · UT Austin

Considered and rejected

Considered and rejected: Discarded 12 primary screening hit compounds because they inhibited transgenic Dd2-ScDHODH >40% at 0.2 uM, indicating off-target cellular activity.

Pre-clinical studies characterizing the evolutionary dynamics of resistance to novel antimalarials in Plasmodium falciparum · Harvard · PhD

Tried and failed

covalent fragment-based screening for protein inhibition applied to pro-apoptotic membrane pore-forming protein. Reason: hit compounds induced non-specific membrane lysis at micromolar concentrations independently of target inhibition

Covalent Inhibition of Pro-Apoptotic BAX · Harvard · PhD

Considered and rejected

Considered and rejected: Rejected using the direct spTorA-mTurquoise2 periplasmic translocation assay for high-throughput Tat inhibitor screening due to insufficient fluorescent assay sensitivity.

PQS-dependent quorum sensing in pseudomonas aeruginosa is linked to protein export via the twin-arginine translocation (tat) system · Nottingham · PhD

Considered and rejected

Considered and rejected: Discontinued SPR screening for small-molecule KD determination after recurring sensorgram distortions and non-saturating kinetics.

The development and evaluation of PET imaging agents targeting PD-L1 · Imperial · PhD

Considered and rejected

Considered and rejected: Rejected 1H NMR (1D NOESY and 2D J-RES) for high-throughput drug-bacteria screening due to insufficient sensitivity at 20 µM drug concentrations and severe matrix overlap from growth media.

Pharmacomicrobiomics in gastrointestinal cancer: the gut microbiome as modulator of anticancer therapy efficacy and predictor of therapy outcomes · Imperial · PhD

Considered and rejected

Considered and rejected: Rejected 96-well micro-well titer plates for persistence screening due to non-adherence of bacteria and the inability to dynamically exchange media during antibiotic treatment and washout

Identification of genes required for host-cell adhesion and antibiotic persistence of uropathogenic Escherichia coli via high-content screening · EPFL · PhD

Tried and failed

activity-based protein profiling validation of screening hits applied to deubiquitinating enzyme inhibitor discovery. Outcome: did not generalise. Reason: in vitro biochemical enzyme inhibition failed to translate to target engagement in cellular lysates

Identification of a privileged scaffold to accelerate DUB drug discovery · Harvard · PhD

Considered and rejected

Considered and rejected: Discarded 29 primary enzymatic screening hits from further evaluation due to poor whole-cell potency (<40% inhibition at 20 uM against both 3D7-WT and 3D7-DHODH:E182D).

Pre-clinical studies characterizing the evolutionary dynamics of resistance to novel antimalarials in Plasmodium falciparum · Harvard · PhD

Tried and failed

screening liquid culture broth for secreted antimicrobial activity applied to bacterial isolates from natural microbiome samples. Outcome: no signal. Reason: most solid-media active isolates failed to produce or excrete active compounds in liquid culture broth

HONEY MICROBIOME AND METABOLOME: A VAST RESERVOIR OF NATURAL ANTIMICROBIALS · Cornell · PhD

Tried and failed

3D shape similarity screening and hybrid inhibitor design applied to kinase active site inhibitor optimization. Outcome: no signal. Reason: hybrid analogs and shape-based mimics failed to retain enzymatic phosphorylation inhibition activity

Targeting VRK1: Selective Inhibitors, Chemical Probes, and Biochemical Insights · Harvard · PhD

Considered and rejected

Considered and rejected: Initially focused on developing a selective AKT3-specific inhibitor, but abandoned after database screening revealed no AKT3-selective molecules, redirecting focus to pan-AKT and dual AKT/DNA-PK inhibitors

Targeting AKT and DNA-PK as a therapeutic strategy in platinum resistant high grade serous ovarian cancer · Imperial · PhD

Left open

Formally validate multi-targeted screening hits as bona fide pan-DUB inhibitors using biochemical assays. Blocker: Requires physical screening hit compounds and wet-lab biochemical validation assays

Discovery and Development of Novel Deubiquitinase Inhibitors via Parallel High-Throughput Screening · Harvard · PhD

Left open

Determine if SteE interacts with and directs phosphorylation on other host kinase substrates using kinase assays or interactome screening. Blocker: Requires wet-lab biochemical assays, protein expression, and kinase interaction screening.

Structural and Functional characterisation of SteE, a Salmonella type III secretion system effector · Imperial · PhD

Left open

Perform kinome profiling and evaluate off-target specificity for the lead reversible inhibitor YKL-04-125. Blocker: Requires wet-lab kinase screening assay panels and physical samples of YKL-04-125.

Biochemical characterization of EGFR exon 20 insertion variants and their inhibitor sensitivities · Harvard · PhD

Left open

Construct in vivo RiPP combinatorial libraries for high-throughput activity-based screening against therapeutic protein-protein interaction targets. Blocker: Requires wet lab facilities, biological reagents, and experimental screening infrastructure

Design of Post-Translationally Modified Peptides by Combining Enzymes from Diverse Pathways · MIT · PhD

Left open

Identify and validate targets for the category 1 and category 3 screening hits from the ΔugtP pathway-directed screen. Blocker: Requires wet-lab experimental biology and biochemistry facilities to validate molecular targets of small molecule hits

Discovery of highly selective inhibitors to probe the physiology of the bacterial cell envelope · Harvard · PhD

Left open

Experimentally evaluate synthesized factorizable mAb libraries via high-throughput screening panning against targets. Blocker: Requires a wet lab and physical reagents for high-throughput screening of mAb libraries

Safe and Ethical Implementation of Intelligent Systems · MIT · PhD

Left open

Refine and score top virtual screening hits using SILCS-MC, parameterize with the Drude force field, and run MD stability assessments. Blocker: Access to proprietary SILCS-MC software and the specific virtual screening hit list from the thesis.

Computer-Aided Drug Design of G-quadruplex Structures: Harnessing Polarization for Rational Drug Design · Virginia Tech · Doctorate

Left open

Perform high-throughput proteomics screening and train a deep learning model on surface electronics data to predict protein surface azidation. Blocker: Requires wet-lab high-throughput proteomics screening experiments to generate training data.

Azide-Containing Hypervalent Iodine Reagents for Biomolecules Functionalization · EPFL · PhD