Modeling Water Molecules in Protein−Ligand Docking Using GOLD

Background: Human cytosolic sulfotransferases (SULTs) regulate the bioactivities of hundreds of signaling molecules. Results: Mutants define the structural changes that determine substrate selectivity. Conclusion: Substrates enter the active site through a molecular pore that opens and closes in response to nucleotide binding. Significance: SULT selectivity is a fundamental determinant of sulfur biology.

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“…The sulfuryl moiety of PAP and the acceptor (DHEA) were added as visual cues. DHEA was docked into the closed structure using GOLD (32).…”

Section: Resultsmentioning

confidence: 99%

Testing the Sulfotransferase Molecular Pore Hypothesis

Cook

Wang

Almo

et al. 2013

Journal of Biological Chemistry

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“…It also reflects our reluctance to optimize the weighting of the scoring function terms for optimal retrospective performance, aware of the oft-described tradeoffs between retrospective optimization and prospective prediction (49). Finally, it is worth noting that in implementing GIST, we only considered the energetic consequences of displacing ordered waters, and did not model the specific interactions between ligands and such waters, which play a role in most protein-ligand complexes (6,7,38,50,51). Here, such interacting waters, which can appear with a ligand to bridge between it and the protein surface, were only implicitly modeled as high-energy, hard-to-displace regions.…”

Section: Discussionmentioning

confidence: 99%

“…More problematic still is when a new bridging water mediates interactions between the ligand and the receptor. Because the energetics of bound water molecules have been challenging to calculate and bridging waters hard to anticipate, large-scale docking of chemical libraries has typically been conducted against artificially desolvated sites or has kept a handful of ordered water molecules that are treated as part of the site, based on structural precedence (5)(6)(7)(8).…”

mentioning

confidence: 99%

Testing inhomogeneous solvation theory in structure-based ligand discovery

Balius

Fischer

Stein

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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Binding-site water is often displaced upon ligand recognition, but is commonly neglected in structure-based ligand discovery. Inhomogeneous solvation theory (IST) has become popular for treating this effect, but it has not been tested in controlled experiments at atomic resolution. To do so, we turned to a grid-based version of this method, GIST, readily implemented in molecular docking. Whereas the term only improves docking modestly in retrospective ligand enrichment, it could be added without disrupting performance. We thus turned to prospective docking of large libraries to investigate GIST's impact on ligand discovery, geometry, and water structure in a model cavity site well-suited to exploring these terms. Although top-ranked docked molecules with and without the GIST term often overlapped, many ligands were meaningfully prioritized or deprioritized; some of these were selected for testing. Experimentally, 13/14 molecules prioritized by GIST did bind, whereas none of the molecules that it deprioritized were observed to bind. Nine crystal complexes were determined. In six, the ligand geometry corresponded to that predicted by GIST, for one of these the pose without the GIST term was wrong, and three crystallographic poses differed from both predictions. Notably, in one structure, an ordered water molecule with a high GIST displacement penalty was observed to stay in place. Inclusion of this water-displacement term can substantially improve the hit rates and ligand geometries from docking screens, although the magnitude of its effects can be small and its impact in drug binding sites merits further controlled studies.water | inhomogeneous solvation theory | ligand discovery | structure-based drug design | docking T he treatment of receptor-bound water molecules, which are crucial for ligand recognition, is a widely recognized challenge in structure-based discovery (1-4). The more tightly bound a water in a site, the greater the penalty for its displacement upon ligand binding, ultimately leading to its retention and the adoption of ligand geometries that do not displace it. More problematic still is when a new bridging water mediates interactions between the ligand and the receptor. Because the energetics of bound water molecules have been challenging to calculate and bridging waters hard to anticipate, large-scale docking of chemical libraries has typically been conducted against artificially desolvated sites or has kept a handful of ordered water molecules that are treated as part of the site, based on structural precedence (5-8).Recently, several relatively fast approaches, pragmatic for early discovery, have been advanced to account for the differential displacement energies of bound water molecules (9-20), complementing more rigorous but computationally expensive approaches (18)(19)(20)(21)(22). Among the most popular of these has been inhomogeneous solvation theory (IST) (23)(24)(25). IST uses populations from molecular dynamics (MD) simulations on protein (solute) surfaces to calculate the cost of di...

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“…The GROMAS57 field was modified in GROMACS to allow the program to recognize the spin-labeled cysteine as a canonical residue. Spin-labeled cysteines were inserted by replacing residues G29, E151, and K234; PAPS was positioned at the active site using GOLD (30)(31)(32); and the system was equilibrated using GROMACS (100-ps increments) to the following simulated condition: 298 K, 50 mM NaCl, and pH 7.4. Once equilibrated, EGCG was positioned randomly in a simulated box of water (52 × 52 × 52 Å) containing the spin-labeled SULT1A1·PAPS construct and then docked in GROMACS using the NMR distance constraints (Positioning EGCG and Results and Discussion).…”

Section: Methodsmentioning

confidence: 99%

The structure of the catechin-binding site of human sulfotransferase 1A1

Cook

Wang

Girvin

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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We are just beginning to understand the allosteric regulation of the human cytosolic sulfotransferase (SULTs) family-13 disease-relevant enzymes that regulate the activities of hundreds, if not thousands, of signaling small molecules. SULT1A1, the predominant isoform in adult liver, harbors two noninteracting allosteric sites, each of which binds a different molecular family: the catechins (naturally occurring flavonols) and nonsteroidal antiinflammatory drugs (NSAIDs). Here, we present the structure of an SULT allosteric binding site-the catechin-binding site of SULT1A1 bound to epigallocatechin gallate (EGCG). The allosteric pocket resides in a dynamic region of the protein that enables EGCG to control opening and closure of the enzyme's active-site cap. Furthermore, the structure offers a molecular explanation for the isozyme specificity of EGCG, which is corroborated experimentally. The bindingsite structure was obtained without X-ray crystallography or multidimensional NMR. Instead, a SULT1A1 apoprotein structure was used to guide positioning of a small number of spin-labeled single-Cys mutants that coat the entire enzyme surface with a paramagnetic field of sufficient strength to determine its contribution to the bound ligand's transverse (T 2 ) relaxation from its 1D solution spectrum. EGCG protons were mapped to the protein surface by triangulation using the T 2 values to calculate their distances to a trio of spin-labeled Cys mutants. The final structure was obtained using distance-constrained molecular dynamics docking. This approach, which is readily extensible to other systems, is applicable over a wide range of ligand affinities, requires little protein, avoids the need for isotopically labeled protein, and has no protein molecular weight limitations.sulfotransferase | structure | NMR | allostery | catechin C ytosolic SULTs regulate disease-relevant process in virtually every tissue in the human body (1-5). This small family of broadspecificity enzymes regulates the activities of hundreds, perhaps thousands, of signaling small molecules (e.g., endogenous metabolites, drugs, and other xenobiotics) via regiospecific transfer of the sulfuryl moiety (-SO 3 ) from 3′-phosphoadenosine 5′-phosphosulfate (PAPS) to the hydroxyls and amines of acceptors (1, 6). Sulfonation often radically alters the interactions of a compound with its target and substantially enhances the target's solubility, transport, and clearance (1, 6, 7). Through these and other mechanisms, SULTs contribute in critical ways to maintaining signaling homeostasis and neutralizing toxins (6,8).Given their wide-ranging roles in regulating cellular processes, it is perhaps expected that SULTs would have evolved means of communicating with their environments-mechanisms that enable them to read and respond to the small-molecule composition of their "milieu." Early screening studies intimated that SULTs might be subject to small-molecule allosteric control (9, 10), and recent work confirms this (11). SULT1A1, the most abundant isoform in adult h...

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Modeling Water Molecules in Protein−Ligand Docking Using GOLD

Cited by 362 publications

References 43 publications

Testing the Sulfotransferase Molecular Pore Hypothesis

Testing the Sulfotransferase Molecular Pore Hypothesis

Testing inhomogeneous solvation theory in structure-based ligand discovery

The structure of the catechin-binding site of human sulfotransferase 1A1

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