Lovastatin lactone may improve irritable bowel syndrome with constipation (IBS-C) by inhibiting enzymes in the archaeal methanogenesis pathway

Abstract

Methane produced by the methanoarchaeon Methanobrevibacter smithii ( M. smithii) has been linked to constipation, irritable bowel syndrome with constipation (IBS-C), and obesity. Lovastatin, which demonstrates a cholesterol-lowering effect by the inhibition of HMG-CoA reductase, may also have an anti-methanogenesis effect through direct inhibition of enzymes in the archaeal methanogenesis pathway. We conducted protein-ligand docking experiments to evaluate this possibility. Results are consistent with recent clinical findings.

Methods: F420-dependent methylenetetrahydromethanopterin dehydrogenase ( mtd), a key methanogenesis enzyme was modeled for two different methanogenic archaea: M. smithii and Methanopyrus kandleri. Once protein models were developed, ligand-binding sites were identified. Multiple ligands and their respective protonation, isomeric and tautomeric representations were docked into each site, including F420-coenzyme (natural ligand), lactone and β-hydroxyacid forms of lovastatin and simvastatin, and other co-complexed ligands found in related crystal structures.

Results: 1) Generally, for each modeled site the lactone form of the statins had more favorable site interactions compared to F420; 2) The statin lactone forms generally had the most favorable docking scores, even relative to the native template PDB ligands; and 3) The statin β-hydroxyacid forms had less favorable docking scores, typically scoring in the middle with some of the F420 tautomeric forms. Consistent with these computational results were those from a recent phase II clinical trial ( NCT02495623) with a proprietary, modified-release lovastatin-lactone (SYN-010) in patients with IBS-C, which showed a reduction in symptoms and breath methane levels, compared to placebo.

Conclusion: The lactone form of lovastatin exhibits preferential binding over the native-F420 coenzyme ligand in silico and thus could inhibit the activity of the key M. smithii methanogenesis enzyme mtd in vivo. Statin lactones may thus exert a methane-reducing effect that is distinct from cholesterol lowering activity, which requires HMGR inhibition by statin β-hydroxyacid forms.

Keywords: IBS; IBS-C; Lovastatin; homology modeling; multi-site docking.

Figure 1.

Modeled quaternary structure of A5UMI1/3IQZB (cyan) and A5UMI1/3IQZF (pink) after respective alignments onto chain-B and chain-F of 3IQZ within PyMOL . 3IQZ’s chain-F is highlighted in silver. Dual chain model site residues (blue surface) were inferred from residues in chain-B and chain-F models that are within 7 Å of the 3IQZ ligand (H4M - white). 3IQZ’s chain-B and chain-F form a quaternary structure with two different H4M binding sites (bottom).

Figure 2.

Best scoring lovastatin-lactone and -hydroxyacid poses in A5UMI1 3IQZB_SiteSeeker2 (top) and Q02394 4JJF_SiteSeeker (bottom). Lovastatin-lactone form is shown with green sticks and hydroxyacid form with red sticks. Residues within 5 angstroms of ligands are labeled. Hydrophilic site residues are shown in cyan and hydrophobic residues in gray.

Figure 3.

Lovastatin-lactone 1: (top) [Calculated affinity: -7.2 (kcal/mol); AutoDock4.1Score: 14.3]; 2: (bottom) F420 [Calculated affinity: -6.99 (kcal/mol); AutoDock4.1Score: 63.3] docked into A5UMI1_3IQZB_SiteSeeker2. Hydrogen bond interactions are denoted with yellow dotted lines.