2-Substituted (N)-Methanocarba A3 Adenosine Receptor Agonists: In Silico, In Vitro, and In Vivo Characterization

Thermal Titration Molecular Dynamics: The Revenge of the Fragments

During the last 20 years, the fragment-based drug discovery approach gained popularity in both industrial and academic settings due to its efficient exploration of the chemical space. This bottom-up approach relies on identifying high-efficiency small ligands (fragments) that bind to a target binding site and then rationally evolve them into mature druglike compounds. To achieve such a task, researchers rely on accurate information about the ligand binding mode, usually obtained through experimental techniques, such as X-ray crystallography or computer simulations. However, the physicochemical characteristics of fragments limit the accuracy and reliability of computational predictions of their binding mode. This article presents a new Thermal Titration Molecular Dynamics (TTMD) protocol, a recently developed enhanced sampling method for qualitatively estimating protein-ligand-binding stability, specifically tuned for the refinement of fragment docking results. The protocol has been applied to eight pharmaceutically relevant targets on 12 different test cases, including ligands with very low molecular weight and structural complexity (MiniFrag/FragLites). In more than 80% of cases, TTMD successfully identified the native fragment binding mode among a set of docking poses, outperforming docking alone and proving to be a useful tool to assist the fragment screening and optimization process.

Potent and Selective Human 5-HT2B Serotonin Receptor Antagonists: 4'-Cyano-(N)-methanocarba-adenosines by Synthetic Serendipity

Rigidified nucleoside derivatives with (N)-methanocarba replacement of ribose have been repurposed as peripheral subtype-selective 5-HT2B serotonin receptor antagonists for heart and lung fibrosis and intestinal/vascular conditions. 4'-Cyano derivative 40 (MRS8209; Ki, 4.27 nM) was 47-fold (human binding, but not rat and mouse) and 724-fold (functionally) selective at 5-HT2BR, compared to antitarget 5-HT2CR, and predicted to form a stable receptor complex using docking and molecular dynamics. 4'-Cyano substituents enhanced 5-HT2BR affinity (typically 4-5-fold compared to 4'-CH2OH), depending on an N6 group larger than methyl. Asymmetric N6 groups (4'-cyano-2-halo derivatives 33-35 and 37) provided potent 5-HT2BR Ki values (7-22 nM). A 4'-CH2CN substituent was less effective than 4'-CN at increasing 5-HT2BR affinity, while a 4'-CHF2 group produced high 5-HT2B affinity/selectivity. A 2-benzylthio-adenine group with unsubstituted 6-NH2 shifted the typical selectivity pattern toward potent 5-HT2C binding. Thus, the SAR suggests that N6-cyclopentyl-4'-cyano modifications are promising, with an interdependence among the substituent positions.

Lipid Trolling to Optimize A3 Adenosine Receptor-Positive Allosteric Modulators (PAMs)

A3 adenosine receptor (A3AR) positive allosteric modulators (PAMs) (2,4-disubstituted-1H-imidazo[4,5-c]quinolin-4-amines) allosterically increase the Emax of A3AR agonists, but not potency, due to concurrent orthosteric antagonism. Following mutagenesis/homology modeling of the proposed lipid-exposed allosteric binding site on the cytosolic side, we functionalized the scaffold, including heteroatom substitutions and exocyclic phenylamine extensions, to increase allosteric binding. Strategically appended linear alkyl-alkynyl chains with terminal amino/guanidino groups improved allosteric effects at both human and mouse A3ARs. The chain length, functionality, and attachment position were varied to modulate A3AR PAM activity. For example, 26 (MRS8247, p-alkyne-linked 8 methylenes) and homologues increased agonist Cl-IB-MECA's Emax and potency ([35S]GTPγS binding). The putative mechanism involves a flexible, terminally cationic chain penetrating the lipid environment for stable electrostatic anchoring to cytosolic phospholipid head groups, suggesting "lipid trolling", supported by molecular dynamic simulation of the active-state model. Thus, we have improved A3AR PAM activity through rational design based on an extrahelical, lipidic binding site.