Fragment-Based Discovery of a Series of Allosteric-Binding Site Modulators of β-Glucocerebrosidase.

β-Glucocerebrosidase (GBA/GCase) mutations leading to misfolded protein cause Gaucher's disease and are a major genetic risk factor for Parkinson's disease and dementia with Lewy bodies. The identification of small molecule pharmacological chaperones that can stabilize the misfolded protein and increase delivery of degradation-prone mutant GCase to the lysosome is a strategy under active investigation. Here, we describe the first use of fragment-based drug discovery (FBDD) to identify pharmacological chaperones of GCase.

Fragment-Based Discovery of Allosteric Inhibitors of SH2 Domain-Containing Protein Tyrosine Phosphatase-2 (SHP2).

The ubiquitously expressed protein tyrosine phosphatase SHP2 is required for signaling downstream of receptor tyrosine kinases (RTKs) and plays a role in regulating many cellular processes. Genetic knockdown and pharmacological inhibition of SHP2 suppresses RAS/MAPK signaling and inhibit the proliferation of RTK-driven cancer cell lines. Here, we describe the first reported fragment-to-lead campaign against SHP2, where X-ray crystallography and biophysical techniques were used to identify fragments binding to multiple sites on SHP2.

The Good, the Bad, and the Twisted Revisited: An Analysis of Ligand Geometry in Highly Resolved Protein-Ligand X-ray Structures.

An analysis of the rotatable bond geometry of drug-like ligand models is reported for high-resolution (<1.1 Å) crystallographic protein-ligand complexes. In cases where the ligand fit to the electron density is very good, unusual torsional geometry is rare and, most often, though not exclusively, associated with strong polar, metal, or covalent ligand-protein interactions.

New active leads for tuberculosis booster drugs by structure-based drug discovery.

The transcriptional repressor EthR from Mycobacterium tuberculosis, a member of the TetR family of prokaryotic homo-dimeric transcription factors, controls the expression of the mycobacterial mono-oxygenase EthA. EthA is responsible for the bio-activation of the second-line tuberculosis pro-drug ethionamide, and consequently EthR inhibitors boost drug efficacy. Here, we present a comprehensive in silico structure-based screening protocol that led to the identification of a number of novel scaffolds of EthR inhibitors in subsequent biophysical screening by thermal shift assay.

Structural and docking studies of potent ethionamide boosters.

Tuberculosis remains the second only to HIV as the leading cause of death by infectious disease worldwide, and was responsible for 1.4 million deaths globally in 2011. One of the essential drugs of the second-line antitubercular regimen is the prodrug ethionamide, introduced in the 1960s.

Computational design of a Diels-Alderase from a thermophilic esterase: the importance of dynamics.

A novel computational Diels-Alderase design, based on a relatively rare form of carboxylesterase from Geobacillus stearothermophilus, is presented and theoretically evaluated. The structure was found by mining the PDB for a suitable oxyanion hole-containing structure, followed by a combinatorial approach to find suitable substrates and rational mutations. Four lead designs were selected and thoroughly modeled to obtain realistic estimates of substrate binding and prearrangement.

Potential and limitations of ensemble docking.

A major problem in structure-based virtual screening applications is the appropriate selection of a single or even multiple protein structures to be used in the virtual screening process. A priori it is unknown which protein structure(s) will perform best in a virtual screening experiment. We investigated the performance of ensemble docking, as a function of ensemble size, for eight targets of pharmaceutical interest.

Validating and understanding ring conformations using small molecule crystallographic data.

Understanding the conformational preferences of ring structures is fundamental to structure-based drug design. Although the Cambridge Structural Database (CSD) provides information on the preferred conformations of small molecules, analyzing this data can be very time-consuming. In order to overcome this hurdle, tools have been developed for quickly extracting geometrical preferences from the CSD.

Pose prediction and virtual screening performance of GOLD scoring functions in a standardized test.

The performance of all four GOLD scoring functions has been evaluated for pose prediction and virtual screening under the standardized conditions of the comparative docking and scoring experiment reported in this Edition. Excellent pose prediction and good virtual screening performance was demonstrated using unmodified protein models and default parameter settings. The best performing scoring function for both pose prediction and virtual screening was demonstrated to be the recently introduced scoring function ChemPLP.

The hydrogen bond environments of 1H-tetrazole and tetrazolate rings: the structural basis for tetrazole-carboxylic acid bioisosterism.

Bioisosterism involving replacement of a carboxylic acid substituent by 1H-tetrazole, yielding deprotonated carboxylate and tetrazolate under physiological conditions, is a well-known synthetic strategy in medicinal chemistry. To improve our overall understanding of bioisosterism, we have used this example to study the geometrical and energetic aspects of the functional group replacement. Specifically, we use crystal structure informatics and high-level ab initio calculations to study the hydrogen bond (H-bond) energy landscapes of the protonated and deprotonated bioisosteric pairs.

The good, the bad and the twisted: a survey of ligand geometry in protein crystal structures.

The protein databank now contains the structures of over 11,000 ligands bound to proteins. These structures are invaluable in applied areas such as structure-based drug design, but are also the substrate for understanding the energetics of intermolecular interactions with proteins. Despite their obvious importance, the careful analysis of ligands bound to protein structures lags behind the analysis of the protein structures themselves.

Designing a new Diels-Alderase: a combinatorial, semirational approach including dynamic optimization.

A computationally inexpensive design strategy involving 'semirational' screening for enzymatic catalysis is presented. The protocol is based on well-established computational methods and represents a holistic approach to the catalytic process. The model reaction studied here is the Diels-Alder, for which a successful computational design has recently been published (Siegel, J.

Computational design of a lipase for catalysis of the Diels-Alder reaction.

Combined molecular docking, molecular dynamics (MD) and density functional theory (DFT) studies have been employed to study catalysis of the Diels-Alder reaction by a modified lipase. Six variants of the versatile enzyme Candida Antarctica lipase B (CALB) have been rationally engineered in silico based on the specific characteristics of the pericyclic addition. A kinetic analysis reveals that hydrogen bond stabilization of the transition state and substrate binding are key components of the catalytic process.

Testing assumptions and hypotheses for rescoring success in protein-ligand docking.

In protein-ligand docking, the scoring function is responsible for identifying the correct pose of a particular ligand as well as separating ligands from nonligands. Recently there has been considerable interest in schemes that combine results from several scoring functions in an effort to achieve improved performance in virtual screens. One such scheme is consensus scoring, which involves combining the results from several rescoring experiments.

Evaluating docking programs: keeping the playing field level.

Over recent years many enrichment studies have been published which purport to rigorously compare the performance of two or more docking protocols. It has become clear however that such studies often have flaws within their methodologies, which cast doubt on the rigour of the conclusions. Setting up such comparisons is fraught with difficulties and no best mode of practice is available to guide the experimenter.

Investigation of the terminal P4 domain in a series of D-phenylglycinamide-based factor Xa inhibitors.

Several P4 domain derivatives of the general d-phenylglycinamide-based scaffold (2) were synthesized and evaluated for their ability to bind to the serine protease factor Xa. Some of the more potent compounds were evaluated for their anticoagulant effects in vitro. A select subset containing various P1 indole constructs was further evaluated for their pharmacokinetic properties after oral administration to rats.

D-phenylglycinol-derived non-covalent factor Xa inhibitors: effect of non-peptidic S4 linkage elements on affinity and anticoagulant activity.

Analogs to a series of D-phenylglycinamide-derived factor Xa inhibitors were discovered. It was found that the S4 amide linkage can be replaced with an ether linkage to reduce the peptide character of the molecules and that this substitution leads to an increase in binding affinity that is not predicted based on modeling. Inhibitors which incorporate ether, amino, or alkyl S4 linkage motifs exhibit similar levels of binding affinity and also demonstrate potent in vitro functional activity, however, binding affinity in this series is strongly dependent on the nature of the S1 binding element.

A four component coupling strategy for the synthesis of D-phenylglycinamide-derived non-covalent factor Xa inhibitors.

A novel isonitrile derivative was synthesized and used in an Ugi four component coupling reaction to explore aryl group substitution effects on inhibition of the coagulation cascade serine protease factor Xa.

PRO_SELECT: combining structure-based drug design and array-based chemistry for rapid lead discovery. 2. The development of a series of highly potent and selective factor Xa inhibitors.

In silico screening of combinatorial libraries prior to synthesis promises to be a valuable aid to lead discovery. PRO_SELECT, a tool for the virtual screening of libraries for fit to a protein active site, has been used to find novel leads against the serine protease factor Xa. A small seed template was built upon using three iterations of library design, virtual screening, synthesis, and biological testing.