Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors

Binding free energies were calculated for the inhibitors lopinavir, ritonavir, saquinavir, indinavir, amprenavir, and nelfinavir bound to HIV-1 protease. An MMPB/SA-type analysis was applied to conformational samples from 3 ns explicit solvent molecular dynamics simulations of the enzyme-inhibitor complexes. Binding affinities and the sampled conformations of the inhibitor and enzyme were compared between different HIV-1 protease protonation states to find the most likely protonation state of the enzyme in the complex with each of the inhibitors. The resulting set of protonation states leads to good agreement between calculated and experimental binding affinities. Results from the MMPB/SA analysis are compared with an explicit/implicit hybrid scheme and with MMGB/SA methods. It is found that the inclusion of explicit water molecules may offer a slight advantage in reproducing absolute binding free energies while the use of the Generalized Born approximation significantly affects the accuracy of the calculated binding affinities.     

Solvation free energies calculated using the GB/SA model: Sensitivity of results on charge sets,protocols, and force fields

The sensitivity of aqueous solvation free energies (SFEs), estimated using the GB/SA continuum solvent model, on charge sets, protocols, and force fields, was studied. Simple energy calculations using the GB/SA solvent model were performed on 11 monofunctional organic compounds. Results indicate that calculated SFEs are strongly dependent on the charge sets. Charges derived from electrostatic potential fitting to high level ab initio wave functions using the CHELPG procedure and “class IV” charges from AM1/CM1a or PM3/CM1p calculations yielded better results than the corresponding Mulliken charges. Calculated SFEs were similar to MC/FEP energies obtained in the presence of explicit TIP4P water. Further improvements were obtained by using GVB/6-31G** and MP2/6-31+G** (CHELPG) charge sets that included correlation effects. SFEs calculated using charge sets assigned by the OPLSA* force field gave the best results of all standard force fields (MM2*, MM3*, MMFF, AMBER*, and OPLSA*) implemented in MacroModel. Comparison of relative and absolute SFEs computed using either the GB/SA continuum model or MC/FEP calculations in the presence of explicit TIP4P water showed that, in general, relative SFEs can be estimated with greater accuracy. A second set of 20 mono- and difunctional molecules was also studied and relative SFEs estimated using energy minimization and thermodynamic cycle perturbation (TCP) protocols. SFEs calculated from TCP calculations using the GB/SA model were sensitive to bond lengths of dummy bonds (i.e., bonds involving dummy atoms). In such cases, keeping the bond lengths of dummy bonds close to the corresponding bond lengths of the starting structures improved the agreement of TCP-calculated SFEs with energy minimization results. Overall, these results indicate that GB/SA solvation free energy estimates from simple energy minimization calculations are of similar accuracy and value to those obtained using more elaborate TCP protocols. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 769–780, 1998     

Molecular modeling for Cu(II)‐aminopolycarboxylate complexes: Structures,conformational energies,and ligand binding affinities

A ligand field molecular mechanics (LFMM) force field (FF) has been developed for d⁹ copper(II) complexes of aminopolycarboxylate ligands. Training data were derived from density functional theory (DFT) geometry optimizations of 14 complexes comprising potentially hexadentate N₂O₄, tetrasubstituted ethylenediamine (ed), and propylenediamine cores with various combinations of acetate and propionate side arms. The FF was validated against 13 experimental structures from X‐ray crystallography including hexadentate N₂O₄ donors where the nitrogens donors are forced to be cis and bis‐tridentate ONO ligands which generate complexes with trans nitrogen donors. Stochastic conformational searches for [Cu{ed(acetate)_n (propionate)_4‐n}]^2?, n = 0–4, were carried out and the lowest conformers for each system reoptimized with DFT. In each case, both DFT and LFMM predict the same lowest‐energy conformer and the structures and energies of the higher‐energy conformers are also in satisfactory agreement. The relative interaction energies for n = 0, 2, and 4 computed by molecular mechanics correlate with the experimental log β binding affinities. Adding in the predicted log β values for n = 1 and 3 suggest for this set of complexes a monotonic decrease in log β as the number of propionate arms increases. © 2013 Wiley Periodicals, Inc.     

Computational Simulation of HIV Protease Inhibitors to the Main Protease (Mpro) of SARS-CoV-2: Implications for COVID-19 Drugs Design

SARS-CoV-2 is highly homologous to SARS-CoV. To date, the main protease (Mpro) of SARS-CoV-2 is regarded as an important drug target for the treatment of Coronavirus Disease 2019 (COVID-19). Some experiments confirmed that several HIV protease inhibitors present the inhibitory effects on the replication of SARS-CoV-2 by inhibiting Mpro. However, the mechanism of action has still not been studied very clearly. In this work, the interaction mechanism of four HIV protease inhibitors Darunavir (DRV), Lopinavir (LPV), Nelfinavir (NFV), and Ritonavire (RTV) targeting SARS-CoV-2 Mpro was explored by applying docking, molecular dynamics (MD) simulations, and MM–GBSA methods using the broad-spectrum antiviral drug Ribavirin (RBV) as the negative and nonspecific control. Our results revealed that LPV, RTV, and NFV have higher binding affinities with Mpro, and they all interact with catalytic residues His41 and the other two key amino acids Met49 and Met165. Pharmacophore model analysis further revealed that the aromatic ring, hydrogen bond donor, and hydrophobic group are the essential infrastructure of Mpro inhibitors. Overall, this study applied computational simulation methods to study the interaction mechanism of HIV-1 protease inhibitors with SARS-CoV-2 Mpro, and the findings provide useful insights for the development of novel anti-SARS-CoV-2 agents for the treatment of COVID-19.     

Voronoi deformation density (VDD) charges: Assessment of the Mulliken, Bader, Hirshfeld, Weinhold, and VDD methods for charge analysis

We present the Voronoi Deformation Density (VDD) method for computing atomic charges. The VDD method does not explicitly use the basis functions but calculates the amount of electronic density that flows to or from a certain atom due to bond formation by spatial integration of the deformation density over the atomic Voronoi cell. We compare our method to the well-known Mulliken, Hirshfeld, Bader, and Weinhold [Natural Population Analysis (NPA)] charges for a variety of biological, organic, and inorganic molecules. The Mulliken charges are (again) shown to be useless due to heavy basis set dependency, and the Bader charges (and often also the NPA charges) are not realistic, yielding too extreme values that suggest much ionic character even in the case of covalent bonds. The Hirshfeld and VDD charges, which prove to be numerically very similar, are to be recommended because they yield chemically meaningful charges. We stress the need to use spatial integration over an atomic domain to get rid of basis set dependency, and the need to integrate the deformation density in order to obtain a realistic picture of the charge rearrangement upon bonding. An asset of the VDD charges is the transparency of the approach owing to the simple geometric partitioning of space. The deformation density based charges prove to conform to chemical experience.     

Synthesis and characterization of manganese(II) and iron(III) d5 tripodal imidazole complexes. Effect of oxidation state, protonation state and ligand conformation on coordination number and spin state

The 1 : 3 Schiff base condensates of tris(2-aminoethyl)amine (tren) or tris(3-aminopropyl)amine (trpn) with 4-methyl-5-imidazolecarboxaldehyde, H3L1 and H3L2, respectively, were generated in situ and used to prepare complexes with manganese(II) and iron(III). The resultant complexes, [MnH3L1](ClO4)2, [MnH3L1](ClO4)2.EtOH.H2O, [MnH3L2](ClO4)2, [FeH3L1](ClO4)3.1.5(EtOH) and [FeHL1](I3) (0.525)(I)(0.475).2.625H2O, have been characterized by EA, IR, ES MS, variable temperature magnetic susceptibility, X-ray crystallography, and M?ssbauer spectroscopy for the iron complexes. The three manganese(II) complexes are high spin with [MnH3L2](ClO4)2 exhibiting coordination number seven while the others are six coordinate. [FeH3L1](ClO4)3.1.5(EtOH) has two iron sites, a seven coordinate and a pseudo seven coordinate site. The complex is high spin at room temperature but exhibits a magnetic moment that decreases with temperature corresponding to conversion of one of the sites to low spin. [FeHL1](I3) (0.525)(I)(0.475).2.625H2O is low spin even at room temperature. In the present complexes the apical nitrogen atom, N(ap), of the tripodal ligand is pyramidal and directed toward the metal atom. The data show that the M-N(ap) distance decreases as the oxidation state of the metal increases, as the number of bound imidazole protons on the ligand increases, and as the number of carbon atoms in the backbone of the ligand (tren vs. trpn) increases. In a limiting sense, short M-N(ap) distances result in high spin seven coordinate mono capped octahedral complexes and long M-N(ap) distances result in low spin six coordinate octahedral complexes.     

Effect of a few repeating stereosequences on electrical space charge behavior of poly(methyl methacrylate)

Three films of poly(methyl methacrylate) (PMMA) (samples X, Y, and Z) were prepared by compression molding of purified polymers as polymers having different tacticities. They were exhaustively characterized by ¹H NMR spectroscopy so as to be able to evaluate the differences in content of the repeating stereosequences:… mmrm … (termini of isotactic sequences); …. rrrmr (breaking off syndiotactic sequences; pure heterotactic … mrmr … moistures; and atactic parts. By applying the so‐called thermal step method, the behavior in space charge showed a priority charge injection from both electrodes and some polarization at the cathode. Some strong differences between the samples were evidenced and they accurately agree with the variations in the above repeating stereosequences for the samples. The results allow to define every stereosequence as specific trap of the distinct sorts of space charge, namely injection from the anode or the cathode and polarization. These attributions are common with those proposed for poly(vinyl chloride) (PVC) and poly(propylene) (PP) in earlier work. Conversely, whether the priority charge is of injection or polarization type, depends markedly on the type of polymer. © 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47: 633–639, 2009     

Excited state properties, fluorescence energies, and lifetime of a poly(fluorene-pyridine) copolymer, based on TD-DFT investigation

The structural and electronic properties of the fluorene-pyridine copolymer (FPy)(n), (n = 1-4) were investigated theoretically by means of quantum mechanical calculations based on density functional theory (DFT) and time-dependent DFT (TD-DFT) using the B3LYP functional. Geometry optimizations of these oligomers were performed for the ground state and the lowest excited state. It was found that (FPy)(n) is nonplanar in its ground state, whereas a more pronounced trend toward planarity is observed in the S(1) state. Absorption and fluorescence energies have been extrapolated to infinite chain length making use of their good linearity with respect to 1/n. An extrapolated value of 2.64 eV is obtained for vertical excitation energy. The S(1)<--S(0) electronic excitation is characterized as a highest occupied molecular orbital to lowest unoccupied molecular orbital transition and is dominating in terms of oscillator strength. Fluorescence energies and radiative lifetime were calculated as well. The obtained results indicate that the fluorescence energy and radiative lifetime of (FPy)(n) are 2.16 eV and 0.38 ns, respectively. The decrease of fluorescence energy and radiative lifetime with the increase in the chain length is discussed.     

New mixed ligand complexes of ruthenium(II) that incorporate a modified phenanthroline ligand: Synthesis, spectral characterization and DNA binding

The hexafluorophosphate and chloride salts of two ruthenium(II) complexes, viz. [Ru(phen)(ptzo)₂]² and [Ru(ptzo)₃]²⁺, where ptzo = 1,10-phenanthrolino[5,6-e]1,2,4-triazine-3-one (ptzo) — a new modified phenanthroline (phen) ligand, have been synthesised. These complexes have been characterised by infrared, UV-Vis, steady-state emission and¹H NMR spectroscopic methods. Results of absorption and fluorescence titration as well as thermal denaturation studies reveal that both thebis- and tris-complexes of ptzo show moderately strong affinity for binding with calf thymus (CT) DNA with the binding constants being close to 10⁵M^-1 in each case. An intercalative mode of DNA binding has been suggested for both the complexes. Emission studies carried out in non-aqueous solvents and in aqueous media without DNA reveal that both [Ru(phen)(ptzo)₂]²⁺ and [Ru(ptzo)₃]²⁺ are weakly luminescent under these solution conditions. Successive addition of CT DNA to buffered aqueous solutions containing [Ru(phen)(ptzo)₂]²⁺results in an enhancement of the emission. These results have been discussed in the light of the dependence of the structure-specific deactivation processes of the MLCT state of the metallo-intercalator with the characteristic features of its DNA interaction. In doing so, attempts have been made to compare and contrast its properties with those of the analogous phenanthroline-based complexes including the ones reported by us previously.     

Effect of silica nanoparticles on solid state polymerization of poly(ethylene terephthalate)

In the present study, the effect of silica nanoparticles, on the solid state polycondensation (SSP) kinetics of poly(ethylene terephthalate) (PET) is thoroughly investigated. At silica concentrations less than 1 wt% and reaction temperatures between 200 and 230 °C higher intrinsic viscosity (IV) values were measured, compared to neat PET at all reaction times. However, with 1 wt% of nanosilica (n-SiO₂), the IV increase of the nanocomposites was similar to that of neat PET and a further increase to 5 wt% n-SiO₂ resulted in significantly lower IV values. A simple kinetic model was also employed to predict the time evolution of IV, as well as the carboxyl and hydroxyl content during SSP. The kinetic parameters of the transesterification and esterification reactions were estimated at different temperatures with or without the addition of n-SiO₂. The activation energies of both reactions were determined together with the concentration of inactive end-groups. From the experimental measurements and the theoretical simulation results it was proved that n-SiO₂ in small amounts (less than 1 wt%) enhances both the esterification and transesterification reactions at all studied temperatures acting as a co-catalyst. However, as the amount of nanosilica increases a number of inactive hydroxyl groups were estimated corresponding to participation of these groups in side reactions with the nanosilica particles. These side reactions lead initially to branched PET chains and eventually (5 wt% n-SiO₂ concentration) to crosslinked structures.     

One-pot synthesis,characterization, DNA binding and enzymatic studies of 4-methyl trans-cinnamate zinc(II)-mixed ligand complexes

Four new zinc(II) complexes formulated as [Zn(L)₂] (1), [Zn(L)₂(phen)] (2), [Zn(L)₂(bipy)H₂O] (3), and [Zn(en)₂(H₂O)₂](L)₂(H₂O)₂ (4), where HL = 4-methyl trans-cinnamic acid, bipy = 2,2′-bipyridine, phen = 1,10-phenanthroline, and en = ethylenediamine, have been synthesized and characterized by FT-IR and NMR spectroscopy. Single-crystal XRD revealed distorted square-pyramidal structure for 3 and octahedral for 4. The complexes were screened for DNA interaction via viscommetry and UV–visible spectroscopy. The apparent binding constants were calculated to be 1.18 × 10⁴, 1.26 × 10⁵, 4.64 × 10⁴_, and 1.89 × 10⁴ for 1–4, respectively. The binding propensity to salmon sperm DNA was in the order: K₂ > K₃ > K₄ > K₁. Furthermore, these complexes demonstrated efficient inhibition of alkaline phosphatase, which was attributed to the binding of zinc(II) to the enzyme’s active site.     

Comparison of radii sets,entropy, QM methods,and sampling on MM‐PBSA,MM‐GBSA,and QM/MM‐GBSA ligand binding energies of F. tularensis enoyl‐ACP reductase (FabI)

To validate a method for predicting the binding affinities of FabI inhibitors, three implicit solvent methods, MM‐PBSA, MM‐GBSA, and QM/MM‐GBSA were carefully compared using 16 benzimidazole inhibitors in complex with Francisella tularensis FabI. The data suggests that the prediction results are sensitive to radii sets, GB methods, QM Hamiltonians, sampling protocols, and simulation length, if only one simulation trajectory is used for each ligand. In this case, QM/MM‐GBSA using 6 ns MD simulation trajectories together with GB^neck2, PM3, and the mbondi2 radii set, generate the closest agreement with experimental values (r² = 0.88). However, if the three implicit solvent methods are averaged from six 1 ns MD simulations for each ligand (called “multiple independent sampling”), the prediction results are relatively insensitive to all the tested parameters. Moreover, MM/GBSA together with GB^HCT and mbondi, using 600 frames extracted evenly from six 0.25 ns MD simulations, can also provide accurate prediction to experimental values (r² = 0.84). Therefore, the multiple independent sampling method can be more efficient than a single, long simulation method. Since future scaffold expansions may significantly change the benzimidazole's physiochemical properties (charges, etc.) and possibly binding modes, which may affect the sensitivities of various parameters, the relatively insensitive “multiple independent sampling method” may avoid the need of an entirely new validation study. Moreover, due to large fluctuating entropy values, (QM/)MM‐P(G)BSA were limited to inhibitors’ relative affinity prediction, but not the absolute affinity. The developed protocol will support an ongoing benzimidazole lead optimization program. © 2015 Wiley Periodicals, Inc.     

Synthesis,DNA binding and antitumor activities of some novel polymer–cobalt(III) complexes containing 1,10-phenanthroline ligand

The novel water-soluble polymer–cobalt(III) complex samples, cis-[Co(phen)₂(BPEI)Cl]Cl₂ · 4H₂O (phen = 1,10-phenanthroline, BPEI = branched polyethyleneimine), with different amounts of cobalt complex content in the polymer chain, were prepared by ligand substitution method in water–ethanol medium and characterized by Infra-red, UV–Vis, ¹H NMR spectral and elemental analysis methods. The interaction of these polymer–cobalt(III)-phenanthroline complex samples with calf thymus DNA has been explored using electronic absorption spectroscopy, emission spectroscopy and gel electrophoresis techniques. The presence of multiple small size molecular binding sites, namely, the cobalt(III)–phenanthroline complex moieties, and free amino groups in a single big sized polymer molecule enhanced both the electrostatic and/or van der Waals interaction and partial intercalative bindings with calf thymus DNA. The antitumor activity of a sample of polymer–cobalt(III) complex was determined using HEp-2 cell line and different cell death indicator stains and MTT assay. Many of the cultured HEp-2 cells treated with this complex suffered loss of viability and death mostly through apoptosis as evidenced by the nuclear and cytoplasmic morphology.     

DFT and TDDFT investigations on the ground and excited states for polynuclear platinum(II) complexes containing the rigid phenylacetylide ligand

We have studied the ground and excited states of the three dendritic polynuclear Pt(II) complexes 1-[Cl(PH3)2PtC≡≡ C]-3,5-[HC≡≡ C]C6H3 (1), 1,3-[Cl(PH3)2PtC≡≡ C]2-5-[HC≡≡ C]C6H3 (2), and 1,3,5-[Cl(PH3)2- PtC≡≡ C]3C6H3 (3), by using the B3LYP and UB3LYP methods, respectively. TDDFT approach with the PCM model was performed to predict the emission spectra properties of 1―3 in CH2Cl2 solution. We first predicted the excited-state geometries for the three complexes. With the change of the number of Pt(II) atom, 1―3 show the different geometry structures in both the ground and excited states; fur- thermore, the increase of the metal density from 1 to 3 results in the red shift of the lowest-energy emissions along the series. The luminescent properties of 1 are somewhat different from those of 2 and 3. The emission properties of 2 and 3 are richer than 1. Our conclusion can give a good support for designing the high efficient luminescent materials.     

A close inspection of Ag(I) coordination to molecular baskets. A study of solvation and guest encapsulation in solution and the solid state

Four molecular baskets 1-4, each comprising a modular bowl-shaped platform and a set of distinctive aromatic gates, were synthesized. The gates were made to incorporate a nitrogen heteroatom at different positions, as in 2-4, or without a coordinating nitrogen, as in 1 (Fig. 1). For polydentate 3 and 4, the location of the nitrogen was revealed to have an effect on directing the basket's coordination to Ag(I) cation, and subsequent folding to enclose space. The folded geometries were shown to encompass a helical, Ag(I):3, or C_3v/C_2v symmetrical, Ag(I):4, dynamic arrangement of the gates (from density functional theory). For 2 and 1, however, the presence of Ag(I) caused the sole formation of oligomers and the absence of coordinating interactions, respectively. Variable temperature (VT) ¹H and ¹⁹F NMR measurements of Ag(I):3 did not provide direct evidence for the solvation of its inner space and the encapsulation of the BF_4⁻ counterion. Moreover, CH₃CN or CH₃NC substrates were not found inside of Ag(I):3. The finding is in contrast with the behavior of Cu(I):3, which is known to encapsulate these guests. The intriguing guest selectivity was accounted for by small structural and electronic differences of Ag(I)/Cu(I) folded baskets. The X-ray solid-state structural studies of 2, 3, and 4 revealed the basket's capacity to fill its inner space with small compounds. Thus, 3 was found with an ordered molecule of chloroform, while 4 contained molecules of CH₃OH and H₂O. The basket selectivity for enclosing and positioning guests, in the solid state, was deduced to be guided by their size and weak host-guest and guest-guest noncovalent interactions.     

Synthesis,structures, and characterization of copper(II), nickel(II), and cobalt(III) metal complexes derived from an asymmetric bidentate Schiff-base ligand

An asymmetric bidentate Schiff-base ligand (2-hydroxybenzyl-2-furylmethyl)imine (L–OH) was prepared. Three complexes derived from L–OH were synthesized by treating an ethanolic solution of the appropriate ligand with an equimolar amount of metallic salt. Three complexes, Cu₂(L–O^?)₂Cl₂ (1), Ni(L–O^?)₂ (2) and Co(L–O^?)₃ (3), have been structurally characterized through elemental analysis, IR, UV spectra and thermogravimetric analysis. Single crystal X-ray diffraction shows metal ions and ligands reacted with different proportions 1?:?1, 1?:?2 and 1?:?3, respectively, so copper(II), nickel(II), and cobalt(III) have different geometries.     

Determination of the solubility,dissolution enthalpy and entropy of R-(+)-2-(4-hydroxyphenoxy) propanic acid in different solutions

The solubilities of R-(+)-2-(4-hydroxyphenoxy) propanic acid in acetone, ethyl acetate, acetonitrile, glycol ether, DMF, MIBK, n-butyl alcohol, THF and pyridine were measured at temperatures ranging from 273.15 K to 323.15 K at atmospheric pressure using a laser detecting system. First, the solubility data of R-(+)-2-(4-hydroxyphenoxy) propanic acid in selected solution were compared by the solubility parameter. Then, the solubility data were correlated by the Buchowski–Ksiazczak λh equation and modified Apelblat equation. Compared with the Apelblat equation, the Buchowski–Ksiazczak λh equation can fit the solubility data well. The dissolution enthalpy, entropy and Gibbs free energy of R-(+)-2-(4-hydroxyphenoxy) propanic acid were predicted by the van’t Hoff and Gibbs equation.     

A mononuclear nickel(II) complex based on polypyridyl ligand: synthesis,characterization, and biological activity

[Ni(acac)₂(o-NPIP)](CH₃OH)₃ (acac = acetylacetonate), based on the polypyridyl ligand 2-(2-nitrophenyl)imidazo[4,5-f]1,10-phenanthroline) (o-NPIP), has been synthesized and characterized by single-crystal analysis, IR and electronic spectra. In the structure of Ni(II) complex, the coordination sphere around Ni(II) is distorted octahedral with one o-NPIP and two acetylacetonates. DNA binding and human serum albumin (HSA) interactions with the Ni(II) complex have been investigated by electronic absorption and fluorescence measurements, revealing that the Ni(II) complex binds with DNA via intercalative binding. The quenching constants verified a dynamic quenching mechanism between HSA and the Ni complex by fluorescence quenching. ΔG, ΔH, and ΔS at different temperatures (288, 298, and 310 K) indicated that hydrophobic interactions play a major role. Synchronous fluorescence spectral experiments revealed that the Ni(II) complex affected the microenvironment around the tryptophan residue of HSA.