Different Binding Modes of Small and Large Binders of GAT1

Abstract

Well-known inhibitors of the γ-aminobutyric acid (GABA) transporter GAT1 share a common scaffold of a small cyclic amino acid linked by an alkyl chain to a moiety with two aromatic rings. Tiagabine, the only FDA-approved GAT1 inhibitor, is a typical example. Some small amino acids such as (R)-nipecotic acid are medium-to-strong binders of GAT1, but similar compounds, such as proline, are very weak binders. When substituted with 4,4-diphenylbut-3-en-1-yl (DPB) or 4,4-bis(3-methylthiophen-2-yl)but-3-en-1-yl (BTB) groups, the resulting compounds have similar pKi and pIC50 values, even though the pure amino acids have very different values. To investigate if small amino acids and their substituted counterparts share a similar binding mode, we synthesized butyl-, DPB-, and BTB-substituted derivatives of small amino acids. Supported by the results of docking studies, we propose different binding modes not only for unsubstituted und substituted, but also for strong- and weak-binding amino acids. These data lead to the conclusion that following a fragment-based approach, not pure but N-butyl-substituted amino acids should be used as starting points, giving a better estimate of the activity when a BTB or DPB substituent is added.

MS‐Based Screening of 5‐Substituted Nipecotic Acid Derived Hydrazone Libraries as Ligands of the GABA Transporter 1

“…Despite these failures, the substitution of positions different from the amino function (e.g., in compounds 6 and 7 ) appears to be an interesting means for the development of potential new GABA uptake inhibitors. Based on molecular modeling the unsubstituted ( R )‐nipecotic acid [( R )‐ 6 ] preferably adopts a binding pose in which the piperidine nitrogen atom faces the intracellular side, whereas for the larger inhibitor tiagabine ( 2 ) the binding pose of the piperidine ring is switched with the nitrogen and the attached arylalkyl residue facing the extracellular side of the transporter . On the basis of these results, we concluded that substitutions particularly at positions 4 or 5 with an appropriate spacer and lipophilic residue could yield GABA uptake inhibitors in which the binding pose of the piperidine ring is retained relative to that of unsubstituted ( R )‐ 6 .…”

Identification of Pyrrolidine‐3‐acetic Acid Derived Oximes as Potent Inhibitors of γ‐Aminobutyric Acid Transporter 1 through Library Screening with MS Binding Assays

“…A prominent selective inhibitor of mGAT1 is the nipecotic acid derivative tiagabine ( 5 ), which is in clinical use (pIC 50 =6.88±0.12; Figure ) . Further examples with enhanced affinity toward mGAT1 are NO711 and DDPM‐2571, which are derived from 3 with an oxime functionality in the alkyl side chain (NO711: pIC 50 =6.83±0.06; DDPM‐2571: pIC 50 =8.27±0.03; Figure ).…”

“…Whereas various studies describe inhibitors of mGAT1 with nipecotic acid and guvacine substructures, only a few are known concerning mGAT1 inhibitors derived from pyrrolidine‐3‐acetic acid ( 4 ). Nevertheless, the preparations of miscellaneous pyrrolidine‐3‐acetic acid derivatives containing different lipophilic residues linked by alkyl, alkenyl, or alkynyl chains to the pyrrolidine nitrogen have been reported since the late 1980s; most examples are provided by a patent, but the pharmacological characterizations at GABA transporters are rather limited . One example is the racemic N ‐(4,4‐diphenylbut‐3‐en‐1‐yl) derivative of pyrrolidine‐3‐acetic acid, ( R , S )‐ 8 , and its enantiomer, ( S )‐ 8 , which were found to be potent and selective GABA uptake inhibitors of a GABA transporter corresponding to mGAT1 in the case of ( R , S )‐ 8 and mGAT1 for ( S )‐ 8 (( R , S )‐ 8 : IC 50 =0.12 (0.10–0.15) μ m determined on rat brain tissue, which is known to preferentially contain the rGAT subtype 1; ( S )‐ 8 : pIC 50 =5.99±0.11; Figure ).…”

“…Nevertheless, the preparations of miscellaneous pyrrolidine‐3‐acetic acid derivatives containing different lipophilic residues linked by alkyl, alkenyl, or alkynyl chains to the pyrrolidine nitrogen have been reported since the late 1980s; most examples are provided by a patent, but the pharmacological characterizations at GABA transporters are rather limited . One example is the racemic N ‐(4,4‐diphenylbut‐3‐en‐1‐yl) derivative of pyrrolidine‐3‐acetic acid, ( R , S )‐ 8 , and its enantiomer, ( S )‐ 8 , which were found to be potent and selective GABA uptake inhibitors of a GABA transporter corresponding to mGAT1 in the case of ( R , S )‐ 8 and mGAT1 for ( S )‐ 8 (( R , S )‐ 8 : IC 50 =0.12 (0.10–0.15) μ m determined on rat brain tissue, which is known to preferentially contain the rGAT subtype 1; ( S )‐ 8 : pIC 50 =5.99±0.11; Figure ). Additionally, ( S )‐pyrrolidine‐3‐acetic acid containing a 4,4‐bis(3‐methylthiophen‐2‐yl)but‐3‐en‐1‐yl residue, (( S )‐ 9 ), was recently examined for its activity at mGAT1, and showed also a high inhibitory potency (( S )‐ 9 : pIC 50 =6.69±0.01, Figure ), whereby the pIC 50 value of tiagabine‐like derivative ( S )‐ 9 is only slightly lower than that of 5 itself .…”

Determination of enantiomeric excess of nipecotic acid as 1‐(7‐nitrobenzo[c][1,2,5]oxadiazol‐4‐yl) derivatives

“…Nitrobenzo[c][1,2,5]oxadiazol-4-yl)piperidine-3-carboxylic acid (rac-5): According to GP with racnipecotic acid (rac-1) (26.0 mg, 0.201 mmol) in aqueous solution of Na 2 CO 3 (9.6 ml) and NBD-F (40.5 mg, 0.221 mmol) in CH 3 CN (3 ml). TLC: R f = 0.12 (CH3 CN/ CH 3 OH = 95:5). TLC: R f = 0.12 (CH3 CN/ CH 3 OH = 95:5).…”