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Small Molecule Highlights #02 – November 2022

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Today’s post features eight (8) new molecules published this month that span a diverse list of drug targets: FFARs, CDK, SARS-CoV-Mpro, CatL, ALK, cMET, DGAT2, CaMKIIα, etc.

These molecules (and their associated research articles) profile several useful drug design strategies, including macrocyclization, dual-mode inhibition mechanisms, covalency, and the use of ligand-based pharmacophore models during HitID campaigns.

This blog was created to highlight progress in target-oriented drug discovery and new potential therapeutic opportunities.

Dalriada Small Molecule Highlights 02 - one pager
Small Molecule Highlights #02 – November 2022

Compound 83

Dalriada Small Molecule Highlights 02 - Compound 83
Compound 83

Compound 83: First-in-class dual-acting allosteric modulator of free fatty acid receptors (FFAR1/4) based on a 1,3,5-triazine-2-amine core-scaffold. FFARs (as GPCRs) have been implicated in various metabolic and inflammatory disorders (e.g. type-2 diabetes mellitus, T2DM). Biochemical potencies against FFAR1, and FFAR2 reported as IC50 = 1, 2 nM, respectively (representing an improvement relative to reference compound TAK-875). Metabolic instability (Liver S9 T1/2 = 1.9 mins) is suggested to stem from triazine-core degradation mechanism, with authors citing the need for further studies.

Reference: https://doi.org/10.1021/acsmedchemlett.2c00160

Compound 42

Dalriada Small Molecule Highlights 02 - Compound 42
Compound 42

Compound 42: Computer-aided drug design (CADD) via a large virtual library (N > 200K), pharmacophore models, and receptor-ligand docking experiments, identified a hit (compound 8) with a measurable inhibitory profile against cyclin-dependent kinases 6 (CDK6), IC50 = 3.7 μM. Medicinal chemistry efforts, ultimately generated compound 42, a CDK4/6 inhibitor (IC50 = 10/16 nM, ~200x improvement). In vivo pharmacokinetic studies revealed; F (%)o. (rats) = 43%, T1/2 = 3.5 hr, along with in vivo efficacy in a Balb/C MCF-7 (breast cancer) xenograft mouse model (100-150 mg/kg).

Reference: https://doi.org/10.1021/acs.jmedchem.2c00947


Dalriada Small Molecule Highlights 02 - SM141

SM141: Peptide-based dual inhibitor of the SARS-CoV2 Main protease (MPro) and Cathepsin L (CatL), with a reported IC50 of 900 nM, and 60 nM, respectively. Covalent mechanism of action against MPro, targeting active site Cys145 via acrylate electrophile. Selectivity was highlighted with minimal inhibition of related viral proteases (e.g. papain-like protease, PLPro), as well as cathepsin B (CatB) (both IC50 > 50 μM). Co-crystal resolved with MPro (PDB 7MB0). Cellular anti-viral activity observed in A549-hACE2 cells (IC50 = 8.2 nM), with intranasal (NAS) administration improving survival in K18-ACE2 transgenic mice (infected with SARS-CoV2).

Reference: https://doi.org/10.1021/jacs.2c04626


Dalriada Small Molecule Highlights 02 - D6808

D6808: Molecular hybridization and macrocyclization strategies were used to identify D6808, a macrocyclic cMET kinase inhibitor (IC50 = 2.9 nM), with efficacy in MET-amplified Hs746T gastric cancer cells (IC50 = 0.7 nM). Broad cytotoxicity was observed in resistance-relevant Ba/F3-Tpr-Met cells (F1200L, M1250T, H1094Y, F1200I, L1195V), with IC50 values of 4.2, 3.2, 1.0, 39.0, and 33.4 nM, respectively. Macrocycle was generated via pentafluorophenyl diphenylphosphinate (FDPP) mediated amide-bond formation. Co-crystal with cMET resolved (PDB 8GVJ), and kinome selectivity was observed against a panel of 373 kinases (with observed off targets including Axl, and TrkA-C).

Reference: https://doi.org/10.1021/acs.jmedchem.2c00981


Dalriada Small Molecule Highlights 02 - PF-06865571

PF-06865571: A first-in-class systemically acting diacylglycerol acyltransferase (DGAT2) inhibitor, developed for use in non-alcoholic steatohepatitis (with liver fibrosis). Medicinal chemistry efforts were focused on mitigating CYP450-mediated safety risks of previous analogs, along with reducing apparent rates of hepatic clearance. In an enzymatic activity assay, PF-06865571 was reported to have an IC50 of 17.2 nM. Physicochemical analyses of TPSA, and LogD4 found values of 108 Å2, 1.9, respectively. Pharmacokinetic studies found oral bioavailability F (%)rats of 31%, with a reduced apparent HHEP CLint of 3.9 μL/mins/106 cells (relative to previous analog). In vivo efficacy was observed via the reduction of plasma/hepatic triglycerides (TG) levels in relevant rat models (0.3-90 mg/kg, p.o.).

Reference: https://doi.org/10.1021/acs.jmedchem.2c01200


Dalriada Small Molecule Highlights 02 - PH-HTBA

PH-HTBA: Ca2+/calmodulin-dependent kinase II-alpha (CaMKIIα) is a Ser/Thr-specific kinase, with important CNS roles in memory/learning, Ca2+ homeostasis/re-uptake, Cl transport, and T-cell activation. In recent years, it has been cited as an emerging drug target for several neurodegenerative disorders. Given CaMKIIα small molecule inhibitors generally suffer from poor sub-type selectivity, and poor brain penetrance, Ph-HTBA represents a novel, brain-permeable fragment (IC50 = 78 nM), CaMKIIα hub-domain KD (SPR) = 757 nM, with observable thermal stabilization, ΔTm (DSF) = +19.02 oC (at >100 μM). Pharmacokinetic analyses revealed an interesting species variance in hepatic clearance between mouse/human in vitro hepatocyte models, CLint = 65/8.6 μL/mins/106 cells.

Reference: https://doi.org/10.1021/acs.jmedchem.2c00805


Dalriada Small Molecule Highlights 02 - CRBN (FLT3)-8
CRBN (FLT3)-8:

CRBN (FLT3)-8: FMS-like tyrosine kinase 3 (FLT3) with an internal tandem duplication (ITD), generating FLT3-ITD, is the most common driver mutation in AML (incidence in ~25% of all patients). While current FLT3i are efficacious, resistance due to FLT3 reactivation is common in the clinic. One novel approach towards FLT3-ITD inhibition involves the use of proteolysis targeting chimeras (PROTACs), a special class of heterobifunctional small molecules, which are used for intracellular targeted protein degradation (TPD). CRBN(FLT3)-8 is a Gilteritinib (clinical FLT3i) based PROTAC, with a CRBN E3 ligase, and a PEG2 linker. Downregulation of FLT3 reported in both MV4-11/MOLM-14 cells, which was supressed in presence of UPSi (suggesting a UPS-dependent MOA). Relevant cell activity was reported in FLT3-ITD mutant AML lines (MV4-11/MOLM-14), IC50 = 0.9/2.8 nM.

Reference: https://doi.org/10.1021/acsmedchemlett.2c00402

Compound 10K

Dalriada Small Molecule Highlights 02 - Compound 10K
Compound 10K

Compound 10K: Anaplastic lymphoma kinase (ALK) represents a validated drug target for non-small cell lung cancer (NSCLC). Compound 10K is reported as the first boronic-acid containing ALK inhibitor, with an observed ALKL1196M IC50 of 8.4 nM. Computational docking models, suggest the unique boronate-motif forms a H-bond with key Asn or Asp residues. Cytotoxicity was observed in NCI-H2228 cells (IC50 = 520 nM), with in vivo efficacy in a relevant lung cancer xenograft model in nude mice (50 mg/kg, i.g., tumor growth inhibitor rate, TGI = 52%)

Reference: https://doi.org/10.1016/j.bmc.2022.117071

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