Accurate assessment of the strain energy in a protein-bound drug using QM/MM X-ray refinement and converged quantum chemistry

An ongoing question regarding the energetics of protein‐ligand binding has been; what is the strain energy that a ligand pays (if any) when binding to its protein target? The traditional method to estimate strain energy uses force fields to calculate the energy difference between the ligand bound conformation and its nearest local minimum/global minimum on the gas‐phase or aqueous phase potential energy surface. This makes the implicit assumption that the underlying force field as well as the reference crystal structure is accurate. Herein, we use ibuprofen as a test case and compare MMFF and ab initio QM methods to identify the local and global minimum conformations. Nine low energy conformations were identified with HF/6‐31G* geometry optimization in vacuo. We also obtained highly accurate relative energies for ibuprofen's conformational energy surface based on M06/aug‐cc‐pVXZ (X = D and T), MP2/aug‐cc‐pVXZ (X = D and T) and the MP2/CBS method (with and without solvent corrections). Moreover, we curate and re‐refine the ibuprofen‐protein complex (PDB 2BXG) using QM/MM X‐ray refinement approaches (HF/6‐31G* was the QM method and the MM model was the AMBER force field ff99sb), which were compared with the low energy conformers to calculate the strain energy. The result indicates that there was an 88% reduction in ibuprofen conformation strain using the QM/MM refined structure versus the original PDB ibuprofen conformations. Furthermore, our results indicate that, due to its inherent limitations in estimating electrostatic interactions, force fields are not suitable to gauge strain energy for charged drug molecules like ibuprofen. The present work offers a carefully validated conformational potential energy surface for a drug molecule as well as a reliable QM/MM re‐refined X‐ray structure that can be used to test current structure‐based drug design approaches. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Model for the fast estimation of basis set superposition error in biomolecular systems

Basis set superposition error (BSSE) is a significant contributor to errors in quantum-based energy functions, especially for large chemical systems with many molecular contacts such as folded proteins and protein-ligand complexes. While the counterpoise method has become a standard procedure for correcting intermolecular BSSE, most current approaches to correcting intramolecular BSSE are simply fragment-based analogues of the counterpoise method which require many (two times the number of fragments) additional quantum calculations in their application. We propose that magnitudes of both forms of BSSE can be quickly estimated by dividing a system into interacting fragments, estimating each fragment's contribution to the overall BSSE with a simple statistical model, and then propagating these errors throughout the entire system. Such a method requires no additional quantum calculations, but rather only an analysis of the system's interacting fragments. The method is described herein and is applied to a protein-ligand system, a small helical protein, and a set of native and decoy protein folds.     

From Primary Silylphosphanes and Arsanes to Novel Group 13–15 Clusters

Abstract

The reaction of the primary silylphosphanes and -arsanes 1 with [LiAlH₄] leads. under evolution of H2 and depending on the solvent, to the different unusual clusters 2 and 3. Compound 2 has a rhombododecahedral skeleton. Surprisingly, the same reaction of the starting materials in DME instead of Et₂O as solvent hrnishes the triple ion pair 3.     

Photoinduced CO release, cellular uptake and cytotoxicity of a tris(pyrazolyl)methane (tpm) manganese tricarbonyl complex

Cell viability studies of HT29 colon cancer cells treated with the CO-releasing compound [Mn(CO)(3)(tpm)]PF(6) revealed a significant photoinduced cytotoxicity comparable to that of established agent 5-fluorouracil (5-FU), while controls kept in the dark were unaffected at up to 100 microM.     

Active peroxo titanium complexes: syntheses, characterization and their potential in the photooxidation of 2-propanol

Two novel peroxo titanium complexes, Li(2)(NH(4))(4)[Ti(2)(O(2))(2)(cit)(Hcit)](2).5H(2)O and Zn(NH(4))(4)[Ti(4)(O(2))(4)(Hcit)(2)(cit)(2)].12H(2)O (cit = citrate), show encouraging results in the photochemical oxidation of 2-propanol.     

Quantum mechanical and molecular dynamics simulations of ureases and Zn beta-lactamases

Herein we briefly review theoretical contributions that have increased our understanding of the structure and function of metallo-beta-lactamases and ureases. Both are bimetallic metalloenzymes, with the former containing two zinc ions and the latter containing two nickel ions. We describe the use of several different methodologies, including quantum chemical calculations, molecular dynamic simulations, as well as mixed QM/MM approaches and how they have impacted our understanding of the structure and function of metallo-beta-lactamases and ureases.     

Isoindoles and dihydroisoquinolines by gold-catalyzed intramolecular hydroamination of alkynes

The title compounds are enantioselectively synthesized in just two preparative steps, making use of the Ugi-four-component reaction with an amino acid as chiral component, followed by a gold-catalyzed hydroamination.     

Reversible Phase Transitions in a Buckybowl Monolayer

Like penguins on ice , buckybowl molecules move closer together when cooled on a copper surface (see model of a corannulene molecule adsorbed on Cu(111)). Upon heating, the molecules spread out into the original crystal phase again. The lower density at room temperature can be explained by the increase in entropy owing to the excitation of bowl vibrations at the surface.