Sandbox

Background

Members of the organic anion transporter (OAT) family, including OAT1, are expressed on the epithelial membrane of the kidney, liver, brain, intestine, and placenta. OAT1 regulates the transport of organic anion drugs from the blood into kidney epithelial cells by utilizing the α-ketoglutarate (α-KG) gradient across the membrane established by the tricarboxylic acid (TCA) cycle.The organic anion transporter 1 (OAT1) also plays a key role in excreting waste from organic drug metabolism and contributes significantly to drug-drug interactions and drug disposition. However, the structural basis of specific substrate and inhibitor transport by human OAT1 (hOAT1) has remained elusive. Here are four cryo-electron microscopy (cryo-EM) structures of hOAT1 in its inward-facing conformation: the apo form, the substrate (olmesartan)-bound form with different anions, and the inhibitor (probenecid)-bound form.

Cryo-EM structure of hOAT1

The apo state structure of human Organic Anion Transporter 1 (hOAT1), determined by cryo-EM, reveals the transporter in an inward-facing conformation. This means the central substrate-binding cavity is open toward the intracellular side of the membrane, ready to release a substrate or accept one from the cytoplasm.

Key Structural Characteristics:

• Overall Fold:

• Adopts the classic Major Facilitator Superfamily (MFS) fold.

• Comprises 12 transmembrane helices (TMs 1-12).

• Exhibits pseudo-two-fold symmetry, divided into an N-lobe (TMs 1-6) and a C-lobe (TMs 7-12).

• Central Binding Cavity:

• The cavity is located between the N-lobe (formed by TM1, TM2, TM4, TM5) and the C-lobe (formed by TM7, TM8, TM10, TM11).

• It possesses a positively charged electrostatic environment, which explains its strong preference for transporting anionic substrates.

• The cavity is lined by 29 residues, forming a hydrophobic and aromatic-rich environment.

• Cavity Borders and Cytosolic Gate:

• The top border (extracellular side) of the cavity is formed by residues including N35, Y230, Y353, and Y354.

• The bottom border (cytosolic side) features a narrow "thin bottom gate" formed by residues M207 and F442. The interaction between these two residues splits the cytosolic entrance into two distinct pathways:

• Path A: Located between TM2 and TM11.

• Path B: Located between TM5 and TM8.

• Conformational State:

• In the apo state, the transporter is in a relaxed, inward-open conformation, providing access for substrates from the cytoplasm.

• The structure serves as a baseline for understanding the conformational changes that occur upon substrate or inhibitor binding.

Olmesartan recognition by hOAT1

The structural and functional analysis of provides a detailed blueprint for substrate specificity and binding.

1. Binding Location and Pose

• Olmesartan binds within the central cavity of hOAT1 in an inward-facing conformation.

• It occupies Site 3 of the binding pocket, which is the primary polyspecific site for anionic substrates.

• The drug adopts a diagonal orientation relative to the membrane plane, a pose that requires more space than the smaller inhibitor probenecid. This orientation is similar to its conformation when bound to the angiotensin receptor.

2. Key Interacting Residues

Olmesartan is surrounded by residues from multiple transmembrane helices (TM1, TM4, TM5, TM7, TM10, TM11) within a 5 Å distance. The critical interactions involve:

• Aromatic and Hydrophobic Cage:

• The biphenyl group of olmesartan is nestled near residue F438.

• The tetrazole ring is positioned between the bottom-gate residues M207 and F442.

• The imidazole moiety is located close to Y354.

• Critical Role of Y230:

• Upon olmesartan binding, the side chain of Y230 undergoes a vertical rotation to accommodate and interact with the substrate.

• Mutagenesis studies confirm its importance: the Y230F mutation increased the IC₅₀ for olmesartan inhibition from 845.3 nM (Wild Type) to 2.36 µM, indicating a reduction in binding affinity.

• The Bottom Gate Residues (M207 and F442):

• These residues are crucial for high-affinity olmesartan binding.

• The M207A mutant caused a 4-fold reduction in affinity (IC₅₀ = 3.78 µM).

• The F442A mutant caused a dramatic 12-fold reduction in affinity (IC₅₀ = 10.32 µM).

• This suggests these residues not only form a gate but also directly interact with large, transportable substrates like olmesartan.

3. Chloride Ion Coordination is Essential

A key finding is the role of a chloride ion in stabilizing the olmesartan-bound state.

• The Chloride-Binding Site: A chloride ion (or bromide, used for confirmation) is observed coordinated between residues S203, Y230, and R466.

• Indirect Role of S203: While S203 does not directly contact olmesartan, it is critical for chloride coordination. This is a major species-specific difference, as rat OAT1 has an alanine at this position.

• Functional Evidence of Chloride Dependence:

• The IC₅₀ of olmesartan is 2.01 µM in chloride-rich conditions but improves to 0.91 µM in chloride-depleted conditions, suggesting a more complex relationship where chloride may facilitate transport.

• The S203A mutant shows a severe ~5-fold reduction in olmesartan binding affinity specifically in the presence of chloride (IC₅₀: WT = 2.47 µM; S203A = 29.52 µM).

• The S203A-Y230F double mutant has an even more profound effect, increasing the IC₅₀ to 93.30 µM in chloride conditions, highlighting their synergistic role in chloride-dependent substrate binding.

Mechanism of OAT1 inhibition by probenecid

The cryo-EM structure of reveals a dual-mechanism of action that goes beyond simple competition, effectively arresting the transporter in a restricted state.

1. Binding Mode and Direct Competition

• Probenecid binds at the top of the central cavity, parallel to the membrane plane.

• Its binding site overlaps with both Site 1 (partially) and Site 3.

• It engages in specific, high-affinity interactions with key residues:

• K382 on TM8 forms a hydrogen bond with the carboxylate group of probenecid.

• Y354 on TM7 forms a hydrogen bond with its sulfonyl group.

• Crucially, K382 is also the residue that interacts with the counter-substrate α-ketoglutarate (α-KG), establishing a direct competitive inhibition mechanism by blocking α-KG binding.

2. Conformational Arrest and Cytoplasmic Path Blockage

The primary inhibitory mechanism is a probenecid-induced conformational change that physically blocks substrate access and exit.

• Constriction of the Binding Pocket: Compared to the apo state, the cytoplasmic opening of the binding pocket narrows from ~15 Å to ~12 Å in the probenecid-bound state.

• Dual-Pathway Blockade: The cytosolic entrance is split into two paths. Probenecid binding critically affects both:

• Path A (between TM2 and TM11) is narrowed from ~5 Å to ~4 Å.

• Path B (between TM5 and TM8) is completely blocked.

This structural rearrangement is caused by a slight inward movement of the cytoplasmic ends of TM5, TM8, TM10, and TM11 toward the binding pocket.

3. Locked Conformation

Full Mechanism of Binding and Inhibition in hOAT1

Fig.1. Mechanism of olmesartan binding and conformational inhibition by probenecid

Overall Transport Cycle & Substrate Binding (e.g., Olmesartan)

1. Outward-Facing State (Hypothesized): The transport cycle begins with the transporter in an outward-facing conformation, open to the extracellular space. Substrates and inhibitors from the blood enter the central binding pocket at this stage.

2. Transition to Inward-Facing State: Upon binding a substrate like olmesartan, the transporter undergoes a conformational change to the inward-facing state, which is the conformation captured in this study.

3. Substrate Binding and Chloride Coordination in the Inward-Open State:

• Olmesartan docks into Site 3, the polyspecific substrate-binding site, engaging a cage of hydrophobic and aromatic residues (e.g., F438, Y354).

• Its binding induces specific structural rearrangements, most notably a vertical rotation of the Y230 side chain.

• Crucially, olmesartan binding creates a favorable environment for chloride ion coordination. The chloride ion is stabilized by a network involving S203, the rotated Y230, and R466.

• This chloride coordination, facilitated by the species-specific residue S203, is essential for high-affinity binding and efficient translocation of olmesartan. The bottom-gate residues M207 and F442 also interact with the drug, potentially playing a role in its final release into the cytoplasm.

4. Substrate Release: The inward-facing conformation with its open paths (Path A and Path B) allows the substrate to dissociate into the cytoplasm. The transporter then likely resets to the outward-facing state, driven by the exchange with intracellular α-ketoglutarate (α-KG).

Inhibition Mechanism (e.g., Probenecid)

The inhibitor probenecid exploits the transport cycle but arrests it through a dual mechanism:

1. Binding and Competition:

• Probenecid enters the binding pocket from the extracellular side and binds in the inward-facing conformation.

• It occupies Site 3 and partially extends into Site 1. In Site 1, it directly competes with the counter-substrate α-KG by forming a key hydrogen bond with K382, a residue critical for α-KG binding.

2. Conformational Arrest and Cytoplasmic Blockade:

• This is the primary inhibitory mechanism. Probenecid binding induces subtle but critical conformational changes in the cytoplasmic regions of TM5, TM8, TM10, and TM11.

• These helices shift inward, causing a constriction of the entire cytoplasmic opening of the binding pocket.

• This constriction completely blocks Path B and severely narrows Path A.

• By physically obstructing these cytosolic paths, probenecid achieves two things:

• It prevents intracellular substrates from entering the binding pocket.

• It traps the transporter in a locked, inward-facing, apo-like conformation, preventing the conformational changes needed to complete the transport cycle.

Notes & References

1. ↑ Cryo-EM structures of human OAT1 reveal drug binding and inhibition mechanisms https://doi.org/10.1016/j.str.2025.07.019