Structure-based design of low-nanomolar PIM kinase inhibitors.

PIM kinases are implicated in variety of cancers by promoting cell survival and proliferation and are targets of interest for therapeutic intervention. We have identified a low-nanomolar pan-PIM inhibitor (PIM1/2/3 potency 5:14:2nM) using structure based modeling. The crystal structure of this compound with PIM1 confirmed the predicted binding mode and protein-ligand interactions except those in the acidic ribose pocket. We show the SAR suggesting the importance of having a hydrogen bond donor in this pocket for inhibiting PIM2; however, this interaction is not important for inhibiting PIM1 or PIM3. In addition, we report the discovery of a new class of PIM inhibitors by using computational de novo design tool implemented in MOE software (Chemical Computing Group). These inhibitors have a different interaction profile.

Luminescence Properties of ZrO2: Ti Ceramics Irradiated with Electrons and High-Energy Xe Ions.

Samples of ZrO2 ceramics with different concentrations of impurity titanium ions were synthesized by mixing zirconium and titanium oxide powders in different mass ratios. The X-ray diffraction analysis was used to determine the phase composition, lattice parameters, and crystallite size of the ceramics with varying dopant concentrations. Upon irradiation of the samples with 220 MeV Xe ions to a fluence of 1010 ions/cm2, a decrease in the intensity of the pulsed cathodoluminescence band at 2.5 eV was observed. Additionally, ion irradiation resulted in the emergence of a new thermoluminescence peak at 450-650 K attributed to radiation-induced traps of charge carriers. Further analysis revealed that the thermoluminescence curves of samples irradiated with electrons and ions comprise a superposition of several elementary peaks. Notably, a complex non-monotonic dependence of cathodo- and thermoluminescence intensity on titanium concentration was observed, suggesting the influence of concentration quenching and the presence of tunneling transitions.

Novel Red Phosphor of Gd3+, Sm3+ co-Activated AgxGd((2-x)/3)-0.3-ySmyEu3+0.30☐(1-2x-2y)/3WO4 Scheelites for LED Lighting.

Gd3+ and Sm3+ co-activation, the effect of cation substitutions and the creation of cation vacancies in the scheelite-type framework are investigated as factors influencing luminescence properties. AgxGd((2-x)/3)-0.3-ySmyEu3+0.3☐(1-2x)/3WO4 (x = 0.50, 0.286, 0.20; y = 0.01, 0.02, 0.03, 0.3) scheelite-type phases (AxGSyE) have been synthesized by a solid-state method. A powder X-ray diffraction study of AxGSyE (x = 0.286, 0.2; y = 0.01, 0.02, 0.03) shows that the crystal structures have an incommensurately modulated character similar to other cation-deficient scheelite-related phases. Luminescence properties have been evaluated under near-ultraviolet (n-UV) light. The photoluminescence excitation spectra of AxGSyE demonstrate the strongest absorption at 395 nm, which matches well with commercially available UV-emitting GaN-based LED chips. Gd3+ and Sm3+ co-activation leads to a notable decreasing intensity of the charge transfer band in comparison with Gd3+ single-doped phases. The main absorption is the 7F0 → 5L6 transition of Eu3+ at 395 nm and the 6H5/2 → 4F7/2 transition of Sm3+ at 405 nm. The photoluminescence emission spectra of all the samples indicate intense red emission due to the 5D0 → 7F2 transition of Eu3+. The intensity of the 5D0 → 7F2 emission increases from ~2 times (x = 0.2, y = 0.01 and x = 0.286, y = 0.02) to ~4 times (x = 0.5, y = 0.01) in the Gd3+ and Sm3+ co-doped samples. The integral emission intensity of Ag0.20Gd0.29Sm0.01Eu0.30WO4 in the red visible spectral range (the 5D0 → 7F2 transition) is higher by ~20% than that of the commercially used red phosphor of Gd2O2S:Eu3+. A thermal quenching study of the luminescence of the Eu3+ emission reveals the influence of the structure of compounds and the Sm3+ concentration on the temperature dependence and behavior of the synthesized crystals. Ag0.286Gd0.252Sm0.02Eu0.30WO4 and Ag0.20Gd0.29Sm0.01Eu0.30WO4, with the incommensurately modulated (3 + 1)D monoclinic structure, are very attractive as near-UV converting phosphors applied as red-emitting phosphors for LEDs.

Structure-based design technology contour and its application to the design of renin inhibitors.

It is well-known that the structure-based design approach has had a measurable impact on the drug discovery process in identifying novel and efficacious therapeutic agents for a variety of disease targets. The de novo design approach has inherent potential to generate novel molecules that best fit into a protein binding site when compared to all of the computational methods applied to structure-based design. In its initial attempts, this approach did not achieve much success due to technical hurdles. More recently, the algorithmic advancements in the methodologies and clever strategies developed to design drug-like molecules have improved the success rate. We describe a state-of-the-art structure-based design technology called Contour and provide details of the algorithmic enhancements we have implemented. Contour was designed to create novel drug-like molecules by assembling synthetically viable fragments in the protein binding site using a high-resolution crystal structure of the protein. The technology consists of a sophisticated growth algorithm and a novel scoring function based on a directional model. The growth algorithm generates molecules by dynamically selecting only those fragments from the fragment library that are complementary to the binding site, and assembling them by sampling the conformational space for each attached fragment. The scoring function embodying the essential elements of the binding interactions aids in the rank ordering of grown molecules and helps identify those that have high probability of exhibiting activity against the protein target of interest. The application of Contour to identify inhibitors against human renin enzyme eventually leading to the clinical candidate VTP-27,999 will be discussed here.

A highly accurate metadynamics-based Dissociation Free Energy method to calculate protein-protein and protein-ligand binding potencies.

Although seeking to develop a general and accurate binding free energy calculation method for protein-protein and protein-ligand interactions has been a continuous effort for decades, only limited successes have been obtained so far. Here, we report the development of a metadynamics-based procedure that calculates Dissociation Free Energy (DFE) and its application to 19 non-congeneric protein-protein complexes and hundreds of protein-ligand complexes covering eight targets. We achieved very high correlations in comparison to experimental binding free energies for these diverse sets of systems, demonstrating the generality and accuracy of the method. Since structures of most proteins are available owing to the recent success of prediction by artificial intelligence, a general free energy method such as DFE, combined with other methods, can make structure-based drug design a widely viable and reliable solution to develop both traditional small molecule drugs and biologic drugs as well as PROTACS.

Biphenyl/diphenyl ether renin inhibitors: filling the S1 pocket of renin via the S3 pocket.

Structure-based design led to the discovery of a novel class of renin inhibitors in which an unprecedented phenyl ring filling the S1 site is attached to the phenyl ring filling the S3 pocket. Optimization for several parameters including potency in the presence of human plasma, selectivity against CYP3A4 inhibition and improved rat oral bioavailability led to the identification of 8d which demonstrated antihypertensive efficacy in a transgenic rat model of human hypertension.

Optimization of orally bioavailable alkyl amine renin inhibitors.

Structure-guided drug design led to new alkylamine renin inhibitors with improved in vitro and in vivo potency. Lead compound 21a, has an IC(50) of 0.83nM for the inhibition of human renin in plasma (PRA). Oral administration of 21a at 10mg/kg resulted in >20h reduction of blood pressure in a double transgenic rat model of hypertension.

Design and optimization of renin inhibitors: Orally bioavailable alkyl amines.

Structure-based drug design led to the identification of a novel class of potent, low MW alkylamine renin inhibitors. Oral administration of lead compound 21l, with MW of 508 and IC(50) of 0.47nM, caused a sustained reduction in mean arterial blood pressure in a double transgenic rat model of hypertension.

Lessons in PROTAC Design from Selective Degradation with a Promiscuous Warhead.

Inhibiting protein function selectively is a major goal of modern drug discovery. Here, we report a previously understudied benefit of small molecule proteolysis-targeting chimeras (PROTACs) that recruit E3 ubiquitin ligases to target proteins for their ubiquitination and subsequent proteasome-mediated degradation. Using promiscuous CRBN- and VHL-recruiting PROTACs that bind >50 kinases, we show that only a subset of bound targets is degraded. The basis of this selectivity relies on protein-protein interactions between the E3 ubiquitin ligase and the target protein, as illustrated by engaged proteins that are not degraded as a result of unstable ternary complexes with PROTAC-recruited E3 ligases. In contrast, weak PROTAC:target protein affinity can be stabilized by high-affinity target:PROTAC:ligase trimer interactions, leading to efficient degradation. This study highlights design guidelines for generating potent PROTACs as well as possibilities for degrading undruggable proteins immune to traditional small-molecule inhibitors.

SMall Molecule Growth 2001 (SMoG2001): an improved knowledge-based scoring function for protein-ligand interactions.

Computational lead design procedures require fast and accurate scoring functions to rank millions of generated virtual ligands for protein targets. In this article, we present an improved version of the SMoG scoring function, called SMoG2001. This function is based on a knowledge-based approach-that is, the free energy parameters are derived from the observed frequencies of atom-atom contacts in the database of three-dimensional structures of protein-ligand complexes via a procedure based on statistical mechanics. We obtained the statistics from the set of 725 complexes. SMoG2001 reproduces the experimental binding constants of the majority of 119 complexes of the testing set with good accuracy. On similar testing sets, SMoG2001 performs better than two other widely used scoring functions, PMF and SCORE1(LUDI), and comparably to DrugScore. SMoG2001 poorly predicts the affinities of ligands interacting via quantum mechanical forces with metal ions and ligands that are large and flexible. We attribute significant improvement in accuracy over previous versions of the SMoG scoring function to a better description of the reference state-that is, the state of no interactions.

Discovery of VTP-27999, an Alkyl Amine Renin Inhibitor with Potential for Clinical Utility.

Structure guided optimization of a series of nonpeptidic alkyl amine renin inhibitors allowed the rational incorporation of additional polar functionality. Replacement of the cyclohexylmethyl group occupying the S1 pocket with a (R)-(tetrahydropyran-3-yl)methyl group and utilization of a different attachment point led to the identification of clinical candidate 9. This compound demonstrated excellent selectivity over related and unrelated off-targets, >15% oral bioavailability in three species, oral efficacy in a double transgenic rat model of hypertension, and good exposure in humans.

From knowledge-based potentials to combinatorial lead design in silico.

Computational methods are becoming increasingly used in the drug discovery process. In this Account, we review a novel computational method for lead discovery. This method, called CombiSMoG for "combinatorial small molecule growth", is based on two components: a fast and accurate knowledge-based scoring function used to predict binding affinities of protein-ligand complexes, and a Monte Carlo combinatorial growth algorithm that generates large numbers of low-free-energy ligands in the binding site of a protein. We illustrate the advantages of the method by describing its application in the design of picomolar inhibitors for human carbonic anhydrase.

Combinatorial computational method gives new picomolar ligands for a known enzyme.

Combinatorial small molecule growth algorithm was used to design inhibitors for human carbonic anhydrase II. Two enantiomeric candidate molecules were predicted to bind with high potency (with R isomer binding stronger than S), but in two distinct conformations. The experiments verified that computational predictions concerning the binding affinities and the binding modes were correct for both isomers. The designed R isomer is the best-known inhibitor (K(d) approximately 30 pM) of human carbonic anhydrase II.