Meilan Huang

Computational identification of self-inhibitory peptides from envelope proteins

Fusion process is known to be the initial step of viral infection and hence targeting the entry process is a promising strategy to design antiviral therapy. The self‐inhibitory peptides derived from the enveloped (E) proteins function to inhibit the protein–protein interactions in the membrane fusion step mediated by the viral E protein. Thus, they have the potential to be developed into effective antiviral therapy. Herein, we have developed a Monte Carlo‐based computational method with the aim to identify and optimize potential peptide hits from the E proteins. The stability of the peptides, which indicates their potential to bind in situ to the E proteins, was evaluated by two different scoring functions, dipolar distance‐scaled, finite, ideal‐gas reference state and residue‐specific all‐atom probability discriminatory function. The method was applied to α‐helical Class I HIV‐1 gp41, β‐sheet Class II Dengue virus (DENV) type 2 E proteins, as well as Class III Herpes Simplex virus‐1 (HSV‐1) glycoprotein, a E protein with a mixture of α‐helix and β‐sheet structural fold. The peptide hits identified are in line with the druggable regions where the self‐inhibitory peptide inhibitors for the three classes of viral fusion proteins were derived. Several novel peptides were identified from either the hydrophobic regions or the functionally important regions on Class II DENV‐2 E protein and Class III HSV‐1 gB. They have potential to disrupt the protein–protein interaction in the fusion process and may serve as starting points for the development of novel inhibitors for viral E proteins. Proteins 2012;

Binding modes of diketo-acid inhibitors of HIV-1 integrase: A comparative molecular dynamics simulation study

Graphical abstract Highlights ► Comparative molecular dynamics simulations on HIV-1 IN bound with L-731,988, L-708,906 and S-1360. ► The acidic end of all the DKA inhibitors studied formed favourable ionic interactions with Lys159. ► The keto–enol parts of these compounds were consistently coordinated to Mg. ► The catalytic residue Glu152 formed a favourable ion–pair interaction with the negatively charged Arg199 on α6 in the most potent DKA inhibitors. ► The complexation with Merck inhibitors and S-1360 significantly constrained the flexible surface loop into an extended or open conformation.

3D-QSAR studies on 4-Hydroxyphenylpyruvate Dioxygenase inhibitors by comparative molecular field analysis (CoMFA)

A comparative molecular field analysis (CoMFA) of alkanoic acid 3-oxo-cyclohex-1-enyl ester and 2-acylcyclohexane-1,3-dione derivatives of 4-hydroxyphenylpyruvate dioxygenase inhibitors has been performed to determine the factors required for the activity of these compounds. The substrates conformation abstracted from dynamic modeling of the enzyme-substrate complex was used to build the initial structures of the inhibitors. Satisfactory results were obtained after an all-space searching procedure, performing a leave-one out (LOO) cross-validation study with cross-validation q(2) and conventional r(2) values of 0.779 and 0.989, respectively. The results provide the tools for predicting the affinity of related compounds, and for guiding the design and synthesis of new HPPD ligands with predetermined affinities.

The role of the active site residues in human galactokinase: implications for the mechanisms of GHMP kinases.

Galactokinase catalyses the phosphorylation of galactose at the expense of ATP. Like other members of the GHMP family of kinases it is postulated to function through an active site base mechanism in which Asp-186 abstracts a proton from galactose. This asparate residue was altered to alanine and to asparagine by site-directed mutagenesis of the corresponding gene. This resulted in variant enzyme with no detectable galactokinase activity. Alteration of Arg-37, which lies adjacent to Asp-186 and is postulated to assist the catalytic base, to lysine resulted in an active enzyme. However, alteration of this residue to glutamate abolished activity. All the variant enzymes, except the arginine to lysine substitution, were structurally unstable (as judged by native gel electrophoresis in the presence of urea) compared to the wild type. This suggests that the lack of activity results from this structural instability, in addition to any direct effects on the catalytic mechanism. Computational estimations of the pK(a) values of the arginine and aspartate residues, suggest that Arg-37 remains protonated throughout the catalytic cycle whereas Asp-186 has an abnormally high pK(a) value (7.18). Quantum mechanics/molecular mechanics (QM/MM) calculations suggest that Asp-186 moves closer to the galactose molecule during catalysis. The experimental and theoretical studies presented here argue for a mechanism in which the C(1)-OH bond in the sugar is weakened by the presence of Asp-186 thus facilitating nucleophilic attack by the oxygen atom on the γ-phosphorus of ATP.

Theoretical studies on tautomerism of benzoylcyclohexane-1,3-dione and its derivatives

Abstract In the present paper, geometry optimizations were performed at HF/6-31G ∗ level for all of the possible tautomers of benzoylcyclohexanedione. For one triketone and two cis -endocyclic double bond enol tautomers that have lowest energies, extensive calculations were performed. The effect of calculation method and the size of the basis set on the relative stability of the tautomers were investigated. In addition, the tautomeric equilibrium constants and the energy barrier of the benzoylcyclohexane-1,3-diones were calculated. The solvent effect was fully considered when calculating the equilibrium constants and the results were analyzed by comparing with the experimental results. Finally, calculations were performed on representative 2-substituted benzoylcyclohexane-1,3-dione derivatives. It appears that the free energy of tautomerization and their HPPD inhibitive activity correlated closely.

Toward a uniform description of hydrogen bonds and halogen bonds: correlations of interaction energies with various geometric, electronic and topological parameters

Halogen bonds, which are specific non-covalent interactions similar to hydrogen bonds, play crucial roles in fields as diverse as supramolecular assemblies, crystal engineering, and biological systems. A total of 108 halogen-bonded and hydrogen-bonded complexes formed by different electron acceptors and NH3, namely, R–A⋯NH3 (A = H, Cl, Br or I), have been investigated at the MP2(full)/aug-cc-pVDZ(-PP) level of theory. The relationships between the interaction strengths and various geometric and electronic structures, as well as topological properties, were established, with a particular focus on the uniformity of these two types of interaction. The dependence of the BSSE-corrected interaction energy (ΔEcor) on the interatomic distance (rA⋯N) appeared to be nonlinear for both halogen-bonded and hydrogen-bonded systems; the relationship between ΔEcor and the difference between rA⋯N and the sum of the van der Waals radii (ΔrA⋯N) can be fitted to a combined quadratic regression equation. Furthermore, we demonstrated that the linear correlations between ΔEcor and ρb(BCP) (the electron density at bond critical points in the A⋯N bond) and its Laplacian ∇2ρb(BCP) can be used to provide a combined description of hydrogen bonds and halogen bonds, with correlation coefficients of 0.964 and 0.956, respectively. The dependence of the interaction strength on the electrostatic potential corresponding to an electron density of 0.002 a.u. along the R–A bond vector (ESP0.002), the amount of charge transferred (QCT) and the second-order perturbation stabilization energies of n(NH3) → σ*(R–A) (E(2)) were also examined. Strong halogen-bonded complexes were found to exhibit different linear correlations from weak halogen-bonded and hydrogen-bonded systems. Nevertheless, for the latter two types of system, a uniform regression equation can be constructed. These relationships not only improve our understanding of the nature of halogen bonding but also provide a feasible approach for predicting or determining the relative strengths of hydrogen bonds and halogen bonds, in particular when both types of non-covalent interaction coexist and compete with each other.

Role of Arg228 in the phosphorylation of galactokinase: the mechanism of GHMP kinases by quantum mechanics/molecular mechanics studies.

GHMP kinases are a group of structurally related small molecule kinases. They have been found in all kingdoms of life and are mostly responsible for catalyzing the ATP-dependent phosphorylation of intermediary metabolites. Although the GHMP kinases are of clinical, pharmaceutical, and biotechnological importance, the mechanism of GHMP kinases is controversial. A catalytic base mechanism was suggested for mevalonate kinase that has a structural feature of the γ-phosphate of ATP close to an aspartate residue; however, for one GHMP family member, homoserine kinase, where the residue acting as general base is absent, a direct phosphorylation mechanism was suggested. Furthermore, it was proposed by some authors that all the GHMP kinases function by a similar mechanism. This controversy in mechanism has limited our ability to exploit these enzymes as drug targets and in biotechnology. Here the phosphorylation reaction mechanism of the human galactokinase, a member of the GHMP kinase family, was investigated using molecular dynamics simulations and density functional theory-based quantum mechanics/molecular mechanics calculations (B3LYP-D/AMBER99). The reaction coordinates were localized by potential energy scan using an adiabatic mapping method. Our results indicate that a highly conserved Glu174 captures Arg105 in the proximity of the α-phosphate of ATP, forming a H-bond network; therefore, the mobility of ATP in the large oxyanion hole is restricted. Arg228 functions to stabilize the negative charge developed at the β,γ-bridging oxygen of the ATP during bond cleavage. The reaction occurs via a direct phosphorylation mechanism, and the Asp186 in the proximity of ATP does not directly participate in the reaction pathway. Because Arg228 is not conserved among GHMP kinases, reagents which form interactions with Arg228, and therefore can interrupt its function in phosphorylation, may be developed into potential selective inhibitors for galactokinase.

beta-1,2,3-Triazolyl-Nucleosides as Nicotinamide Riboside Mimics

The synthesis of a series of pyridine- and piperidine-substituted 1,2,3-triazolides linked to a riboside moiety is described. The presence of a triazolide substituent on the pyridine moiety permitted the facile reduction of the latter under mild hydrogenation conditions. These analogues were modelled as to define their similarity to nicotinamide riboside and quantify their ability to bind NAD-dependent protein deacetylases.

Phosphorylation Mechanism of Phosphomevalonate Kinase: Implications for Rational Engineering of Isoprenoid Biosynthetic Pathway Enzymes

The mevalonate pathway is of important clinical, pharmaceutical, and biotechnological relevance. However, lack of the understanding of the phosphorylation mechanism of the kinases in this pathway has limited rationally engineering the kinases in industry. Here the phosphorylation reaction mechanism of a representative kinase in the mevalonate pathway, phosphomevalonate kinase, was studied by using molecular dynamics and hybrid QM/MM methods. We find that a conserved residue (Ser106) is reorientated to anchor ATP via a stable H-bond interaction. In addition, Ser213 located on the α-helix at the catalytic site is repositioned to further approach the substrate, facilitating the proton transfer during the phosphorylation. Furthermore, we elucidate that Lys101 functions to neutralize the negative charge developed at the β-, γ-bridging oxygen atom of ATP during phosphoryl transfer. We demonstrate that the dissociative catalytic reaction occurs via a direct phosphorylation pathway. This is the first study on the phosphorylation mechanism of a mevalonate pathway kinase. The elucidation of the catalytic mechanism not only sheds light on the common catalytic mechanism of the GHMP kinase superfamily but also provides the structural basis for engineering the mevalonate pathway kinases to further exploit their applications in the production of a wide range of fine chemicals such as biofuels or pharmaceuticals.

The Reaction Mechanism of Isopentenyl Phosphate Kinase: A QM/MM Study

Isopentenyl phosphate kinase (IPK) catalyzes the Mg2+-ATP dependent phosphorylation reactions to produce isopentenyl diphosphate, an important precursor in the synthesis of isopentenols. However, the position of the divalent metal ion in the crystal structures of IPK in complex with ATP and its native substrate IP has not been definitively resolved, and as a result ambiguity surrounds the catalytic mechanism of IP, limiting its exploitation as a biofuel and in drug design. Here we report the catalytically competent structure in complex with the metal ion Mg2+ and elucidate the phosphorylation reaction mechanism using molecular dynamic simulations and density functional theory-based quantum mechanics/molecular mechanics calculations (B97d/AMBER99). Comparing the substrate-bound and substrate-free IPK complexes, we observed that substrate binding results in significant conformational change of three residues Lys204, Glu207, and Lys211 located on the αG helix to form a strong salt bridge network with Asp145, which in turn tethers the invariant Ser142 via H-bond interaction. The conformational change shuts the subtrate entrance channel formed between the αG and αE helices. Further, we demonstrate the phosphorylation reaction occurs with a reaction barrier of 17.58 kcal/mol, which is in agreement with the previous experimental kinetic data. We found that a highly conserved Gly8 on a glycine-rich loop, together with Lys14, stabilizes the transition state.