Rodrigo Galindo-Murillo

Refinement of the Sugar-Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA.

Z-DNA duplexes are a particularly complicated test case for current force fields. We performed a set of explicit solvent molecular dynamics (MD) simulations with various AMBER force field parametrizations including our recent refinements of the ε/ζ and glycosidic torsions. None of these force fields described the ZI/ZII and other backbone substates correctly, and all of them underpredicted the population of the important ZI substate. We show that this underprediction can be attributed to an inaccurate potential for the sugar-phosphate backbone torsion angle β. We suggest a refinement of this potential, β(OL1), which was derived using our recently introduced methodology that includes conformation-dependent solvation effects. The new potential significantly increases the stability of the dominant ZI backbone substate and improves the overall description of the Z-DNA backbone. It also has a positive (albeit small) impact on another important DNA form, the antiparallel guanine quadruplex (G-DNA), and improves the description of the canonical B-DNA backbone by increasing the population of BII backbone substates, providing a better agreement with experiment. We recommend using β(OL1) in combination with our previously introduced corrections, εζ(OL1) and χ(OL4), (the combination being named OL15) as a possible alternative to the current β torsion potential for more accurate modeling of nucleic acids.

Assessing the Current State of Amber Force Field Modifications for DNA

The utility of molecular dynamics (MD) simulations to model biomolecular structure, dynamics, and interactions has witnessed enormous advances in recent years due to the availability of optimized MD software and access to significant computational power, including GPU multicore computing engines and other specialized hardware. This has led researchers to routinely extend conformational sampling times to the microsecond level and beyond. The extended sampling time has allowed the community not only to converge conformational ensembles through complete sampling but also to discover deficiencies and overcome problems with the force fields. Accuracy of the force fields is a key component, along with sampling, toward being able to generate accurate and stable structures of biopolymers. The Amber force field for nucleic acids has been used extensively since the 1990s, and multiple artifacts have been discovered, corrected, and reassessed by different research groups. We present a direct comparison of two of the most recent and state-of-the-art Amber force field modifications, bsc1 and OL15, that focus on accurate modeling of double-stranded DNA. After extensive MD simulations with five test cases and two different water models, we conclude that both modifications are a remarkable improvement over the previous bsc0 force field. Both force field modifications show better agreement when compared to experimental structures. To ensure convergence, the Drew–Dickerson dodecamer (DDD) system was simulated using 100 independent MD simulations, each extended to at least 10 μs, and the independent MD simulations were concatenated into a single 1 ms long trajectory for each combination of force field and water model. This is significantly beyond the time scale needed to converge the conformational ensemble of the internal portions of a DNA helix absent internal base pair opening. Considering all of the simulations discussed in the current work, the MD simulations performed to assess and validate the current force fields and water models aggregate over 14 ms of simulation time. The results suggest that both the bsc1 and OL15 force fields render average structures that deviate significantly less than 1 Å from the average experimental structures. This can be compared to similar but less exhaustive simulations with the CHARMM 36 force field that aggregate to the ∼90 μs time scale and also perform well but do not produce structures as close to the DDD NMR average structures (with root-mean-square deviations of 1.3 Å) as the newer Amber force fields. On the basis of these analyses, any future research involving double-stranded DNA simulations using the Amber force fields should employ the bsc1 or OL15 modification.

Intercalation processes of copper complexes in DNA

The family of anticancer complexes that include the transition metal copper known as Casiopeínas® shows promising results. Two of these complexes are currently in clinical trials. The interaction of these compounds with DNA has been observed experimentally and several hypotheses regarding the mechanism of action have been developed, and these include the generation of reactive oxygen species, phosphate hydrolysis and/or base-pair intercalation. To advance in the understanding on how these ligands interact with DNA, we present a molecular dynamics study of 21 Casiopeínas with a DNA dodecamer using 10 μs of simulation time for each compound. All the complexes were manually inserted into the minor groove as the starting point of the simulations. The binding energy of each complex and the observed representative type of interaction between the ligand and the DNA is reported. With this extended sampling time, we found that four of the compounds spontaneously flipped open a base pair and moved inside the resulting cavity and four compounds formed stacking interactions with the terminal base pairs. The complexes that formed the intercalation pocket led to more stable interactions.

On the absence of intrahelical DNA dynamics on the μs to ms timescale

DNA helices display a rich tapestry of motion on both short (< 100 ns) and long (> 1 ms) timescales. However, with the exception of mismatched or damaged DNA, experimental measures indicate that motions in the 1 µs to 1 ms range are effectively absent, which is often attributed to difficulties in measuring motions in this time range. We hypothesized that these motions have not been measured because there is effectively no motion on this timescale, as this provides a means to distinguish faithful Watson-Crick base paired DNA from damaged DNA. The absence of motion on this timescale would present a “static” DNA sequence-specific structure that matches the encounter timescales of proteins, thereby facilitating recognition. Here we report long timescale (~10-44 µs) molecular dynamics simulations of a B-DNA duplex structure that addresses this hypothesis using both an “Anton” machine and large ensembles of AMBER GPU simulations.

Whole Genome Gene Expression Analysis Reveals Casiopeína-Induced Apoptosis Pathways

Copper-based chemotherapeutic compounds Casiopeínas, have been presented as able to promote selective programmed cell death in cancer cells, thus being proper candidates for targeted cancer therapy. DNA fragmentation and apoptosis–in a process mediated by reactive oxygen species–for a number of tumor cells, have been argued to be the main mechanisms. However, a detailed functional mechanism (a model) is still to be defined and interrogated for a wide variety of cellular conditions before establishing settings and parameters needed for their wide clinical application. In order to shorten the gap in this respect, we present a model proposal centered in the role played by intrinsic (or mitochondrial) apoptosis triggered by oxidative stress caused by the chemotherapeutic agent. This model has been inferred based on genome wide expression profiling in cervix cancer (HeLa) cells, as well as statistical and computational tests, validated via functional experiments (both in the same HeLa cells and also in a Neuroblastoma model, the CHP-212 cell line) and assessed by means of data mining studies.

DNA binding dynamics and energetics of cobalt, nickel, and copper metallopeptides.

We present molecular dynamics (MD) and Quantum Theory of Atoms in Molecules (QTAIM) analysis of the DNA binding properties of three metallopeptides to the Drew–Dickerson dodecamer DNA: CoII‐Gly1‐Gly2‐His, NiII‐Gly1‐Gly2‐His and CuII‐Gly1‐Gly2‐His. Fairly extensive MD simulations were run on each system until a stable binding mode for each ligand was sampled. Clustering analysis was used in an attempt to find representative structures for the most populated clusters sampled during the MD, and a QTAIM analysis was performed. Additionally, MM‐PBSA analysis was performed to obtain approximate binding energies for each complex. The results suggest that stable DNA–metallopeptide complexes are formed with each of the three ligands, and that the most stable interaction is with Co(GGH), then Ni(GGH), and finally Cu(GGH). Bond Critical Points (BCP) information between the minor groove of the DNA and the metallopeptides shows an increase in electronic density between Gly1, the His residues, and the oxygen atoms of the thymine nucleotide. Overall, we present a detailed theoretical study of the specific interactions involved and the binding properties of each complex formed.

In Silico Design of Monomolecular Drug Carriers for the Tyrosine Kinase Inhibitor Drug Imatinib Based on Calix- and Thiacalix[n]arene Host Molecules: A DFT and Molecular Dynamics Study.

The use of functionalized calix- and thia-calix[n]arenes is proposed as the basis for our in silico design of a suitable drug carrier for the tyrosine kinase inhibitor, Imatinib. Their mutual electronic properties and interaction energies, Eint, were assessed with the use of Density Functional Theory (DFT) methods under the NBODel methodology. Three structural variables for the host molecules were considered: R = {SO3H (1), t-Bu (2), i-Pr (3), COOH (4), (CH2)2OH (5), (CH2)2NH2 (6)}; b = {CH2, S}; n = {5, 6, 8}, and two possible orientations for the insertion of Imatinib within the macrocycle cavity: pyridine moiety pointing inward (N1) and piperazine pointing inward (N2). In total, we explored 72 different assemblies. Initial molecular mechanics geometry optimizations with the UFF potential were undertaken for every host-guest complex, with further optimization at the B97D/6-31G(d,p) level of theory. Using the same optimized structures, Molecular Dynamics (MD) simulations were carried out on all 72 assemblies using the General Amber Force Field and the AMBER 12 MD package. Electronic parameters were fitted using the RESP method, and the complexes were run for 100 ns. Potential of mean force was obtained for the most stable systems using umbrella sampling and the Weighted Histogram Analysis Method. Calix[n]arenes families 1 and 5 (R = SO3H and (CH2)2OH, respectively) with n = 6 constitute the most promising candidates to become drug carriers within our parameter space due to their more negative Eint values and increased flexibility to allow the inclusion of the drug.

Oxazinin A, a pseudodimeric natural product of mixed biosynthetic origin from a filamentous fungus.

A racemic, prenylated polyketide dimer, oxazinin A (1), was isolated from a novel filamentous fungus in the class Eurotiomycetes, and its structure was elucidated spectroscopically. The pentacyclic structure of oxazinin A (1) is a unique combination of benzoxazine, isoquinoline, and a pyran ring. Oxazinin A (1) exhibited antimycobacterial activity and modestly antagonized transient receptor potential (TRP) channels.

Transitions of Double-Stranded DNA Between the A- and B-Forms.

The structure of double-stranded DNA (dsDNA) is sensitive to solvent conditions. In solution, B-DNA is the favored conformation under physiological conditions, while A-DNA is the form found under low water activity. The A-form is induced locally in some protein-DNA complexes, and repeated transitions between the B- and A-forms have been proposed to generate the forces used to drive dsDNA into viral capsids during genome packaging. Here, we report analyses on previous molecular dynamics (MD) simulations on B-DNA, along with new MD simulations on the transition from A-DNA to B-DNA in solution. We introduce the A-B Index (ABI), a new metric along the A-B continuum, to quantify our results. When A-DNA is placed in an equilibrated solution at physiological ionic strength, there is no energy barrier to the transition to the B-form, which begins within about 1 ns. The transition is essentially complete within 5 ns, although occasionally a stretch of a few base pairs will remain A-like for up to ∼10 ns. A comparison of four sequences with a range of predicted A-phobicities shows that more A-phobic sequences make the transition more rapidly than less A-phobic sequences. Simulations on dsDNA with a region of roughly one turn locked in the A-form allow us to characterize the A/B junction, which has an average bend angle of 20-30°. Fluctuations in this angle occur with characteristic times of about 10 ns.

A mixed DFT‐MD methodology for the in silico development of drug releasing macrocycles. Calix and thia‐calix[N]arenes as carriers for Bosutinib and Sorafenib

Interaction energies between a family of 36 calix[n]arenes, their corresponding thia‐ analogues, and two commercially available second generation tyrosine kinase III inhibitors—Bosutinib and Sorafenib—were calculated through DFT methods at the B97D/6‐31G(d,p) level of theory, based on Natural Population Analysis, for the in silico development of suitable drug carriers based on the aforementioned macrocycles which can increase their bioavailability and in turn their pharmaceutical efficiency. Molecular Dynamics simulations (production runs: +500 ns) using the General Amber Force Field were also carried out in order to assess the releasing process of these drugs in an explicit aqueous environment. In total, 144 host–guest complexes are examined. According to our results, five‐membered SO3H and i–Pr functionalized‐calixarenes are the best candidates for Sorafenib‐carriers while six‐membered ones SO3H and C2H4NH2 functionalized– are the lead candidates for Bosutinib‐carriers.