Glycine receptor (GlyR) chloride channel, member of the pentameric Cys-loop ligand-gated ion channel family that mediates inhibitory neurotransmission in the spinal cord, retina and brainstem. Probes that specifically enhance α3-containing GlyRs have emerged as potential treatments for inflammatory pain. Previously, we reported that variabilin analogues (Ircinia variabilis) might be useful as prototypes for selective GlyR drug development. Hence, the aim of this study was to identify and characterize its novel synthetic analogues. 107 novel compounds were subjected to automated patch clamp based screening using HEK cells stably expressing homomeric α1 or α3 GlyRs. Initially, 18 hits were identified with compounds that modulated both α1 and α3 GlyR and others that potentiated specifically α1 or α3 GlyRs. CMB-C27-E11 potentiated (EC20 glycine) α1 GlyR at lower doses (0.1μM) but inhibited at higher doses (>30 μM). Whereas, CMB-C27-B10 (EC50 ~0.3μM) was found to potentiate current of both receptors but had a stronger effect on α3. Intrathecal administration of B10 (500 nM) in rats showed moderate increase (40 ± 14%) in maximum possible effect (MPE) (Complete Freud’s adjuvant induced thermal hyperalgesia) with mild motor side effects in rotarod apparatus. Based on B10, 18 new analogues were designed to achieve high α3>>α1 selectivity and were subjected to automated patch clamp screening. Out of these, only CMB-C28-H01 was found to be highly α3 selective with 184 ± 12 % potentiation of EC20 glycine current (α1 GlyR= 91 ± 24 % potentiation). Further, intrathecal administration of H01 (100 nM) in rats showed dose dependent increase in %MPE in inflammation-induced allodynia with less disruption of motor activity. Interestingly, H01 prolonged glycine current decay time for α1 in comparison to α1 GlyRs in artificial synapses. Based on above experiments, we conclude that these synthetic variabilin analogues are potential leads for developing drugs that target specific GlyR isoforms.