25 research outputs found
Supervised Molecular Dynamics (SuMD) as a Helpful Tool To Depict GPCR–Ligand Recognition Pathway in a Nanosecond Time Scale
Supervised MD (SuMD) is a computational
method that allows the
exploration of ligand–receptor recognition pathway investigations
in a nanosecond (ns) time scale.
It consists of the incorporation of a tabu-like supervision algorithm
on the ligand–receptor approaching distance into a classic
molecular dynamics (MD) simulation
technique. In addition to speeding up the acquisition of the ligand–receptor
trajectory, this implementation facilitates the characterization
of multiple binding events (such as meta-binding, allosteric, and
orthosteric sites) by taking advantage of the all-atom MD simulations
accuracy of a GPCR–ligand complex embedded into explicit lipid–water
environment
Supervised Molecular Dynamics (SuMD) as a Helpful Tool To Depict GPCR–Ligand Recognition Pathway in a Nanosecond Time Scale
Supervised MD (SuMD) is a computational
method that allows the
exploration of ligand–receptor recognition pathway investigations
in a nanosecond (ns) time scale.
It consists of the incorporation of a tabu-like supervision algorithm
on the ligand–receptor approaching distance into a classic
molecular dynamics (MD) simulation
technique. In addition to speeding up the acquisition of the ligand–receptor
trajectory, this implementation facilitates the characterization
of multiple binding events (such as meta-binding, allosteric, and
orthosteric sites) by taking advantage of the all-atom MD simulations
accuracy of a GPCR–ligand complex embedded into explicit lipid–water
environment
Supervised Molecular Dynamics (SuMD) as a Helpful Tool To Depict GPCR–Ligand Recognition Pathway in a Nanosecond Time Scale
Supervised MD (SuMD) is a computational
method that allows the
exploration of ligand–receptor recognition pathway investigations
in a nanosecond (ns) time scale.
It consists of the incorporation of a tabu-like supervision algorithm
on the ligand–receptor approaching distance into a classic
molecular dynamics (MD) simulation
technique. In addition to speeding up the acquisition of the ligand–receptor
trajectory, this implementation facilitates the characterization
of multiple binding events (such as meta-binding, allosteric, and
orthosteric sites) by taking advantage of the all-atom MD simulations
accuracy of a GPCR–ligand complex embedded into explicit lipid–water
environment
Supervised Molecular Dynamics (SuMD) as a Helpful Tool To Depict GPCR–Ligand Recognition Pathway in a Nanosecond Time Scale
Supervised MD (SuMD) is a computational
method that allows the
exploration of ligand–receptor recognition pathway investigations
in a nanosecond (ns) time scale.
It consists of the incorporation of a tabu-like supervision algorithm
on the ligand–receptor approaching distance into a classic
molecular dynamics (MD) simulation
technique. In addition to speeding up the acquisition of the ligand–receptor
trajectory, this implementation facilitates the characterization
of multiple binding events (such as meta-binding, allosteric, and
orthosteric sites) by taking advantage of the all-atom MD simulations
accuracy of a GPCR–ligand complex embedded into explicit lipid–water
environment
Perturbation of Fluid Dynamics Properties of Water Molecules during G Protein-Coupled Receptor–Ligand Recognition: The Human A<sub>2A</sub> Adenosine Receptor as a Key Study
Recent
advances in structural biology revealed that water molecules
play a crucial structural role in the protein architecture and ligand
binding of G protein-coupled receptors. In this work, we present an
alternative approach to monitor the time-dependent organization of
water molecules during the final stage of the ligand–receptor
recognition process by means of membrane molecular dynamics simulations.
We inspect the variation of fluid dynamics properties of water molecules
upon ligand binding with the aim to correlate the results with the
binding affinities. The outcomes of this analysis are transferred
into a bidimensional graph called water fluid dynamics maps, that
allow a fast graphical identification of protein “hot-spots”
characterized by peculiar shape and electrostatic properties that
can play a critical role in ligand binding. We hopefully believe that
the proposed approach might represent a valuable tool for structure-based
drug discovery that can be extended to cases where crystal structures
are not yet available, or have not been solved at high resolution
Alternative Quality Assessment Strategy to Compare Performances of GPCR-Ligand Docking Protocols: The Human Adenosine A<sub>2A</sub> Receptor as a Case Study
The
progress made in the field of G protein-coupled receptors (GPCRs)
structural determination has increased the adoption of docking-driven
approaches for the identification or optimization of novel potent
and selective ligands. In this work, we compared the performances
of the 16 different docking/scoring combinations using the recently
released crystal structures of the human A<sub>2A</sub> AR (hA<sub>2A</sub> AR) in complex with both agonists and antagonists. The proposed
evaluation strategy encompasses the use of three complementary “quality
descriptors”: (a) the number of conformations generated by
a docking algorithm having a RMSD value lower than the crystal structure
resolution (R); (b) a novel consensus-based function defined as “protocol
score”; and (c) the interaction energy maps (IEMs) analysis,
based on the identification of key ligand–receptor interactions
observed in the crystal structures
Bridging Molecular Docking to Membrane Molecular Dynamics To Investigate GPCR–Ligand Recognition: The Human A<sub>2A</sub> Adenosine Receptor as a Key Study
G protein-coupled
receptors (GPCRs) represent the largest family
of cell-surface receptors and about one-third of the actual targets
of clinically used drugs. Following the progress made in the field
of GPCRs structural determination, docking-based screening for novel
potent and selective ligands is becoming an increasingly adopted strategy
in the drug discovery process. However, this methodology is not yet
able to anticipate the “bioactive” binding mode and
discern it among other conformations. In the present work, we present
a novel approach consisting in the integration of molecular docking
and membrane MD simulations with the aim to merge the rapid sampling
of ligand poses into in the binding site, typical of docking algorithms,
with the thermodynamic accuracy of MD simulations in describing, at
the molecular level, the stability a GPCR-ligand complex embedded
into explicit lipid–water environment. To validate our approach,
we have chosen as a key study the human A<sub>2A</sub> adenosine receptor
(hA<sub>2A</sub> AR) and selected four receptor–antagonist
complexes and one receptor–agonist complex that have been recently
crystallized. In light of the obtained results, we believe that our
novel strategy can be extended to other GPCRs and might represent
a valuable tool to anticipate the “bioactive” conformation
of high-affinity ligands
Synthesis and preliminary structure-activity relationship study of 2-aryl-2<i>H</i>-pyrazolo[4,3-<i>c</i>]quinolin-3-ones as potential checkpoint kinase 1 (Chk1) inhibitors
<p>The serine-threonine checkpoint kinase 1 (Chk1) plays a critical role in the cell cycle arrest in response to DNA damage. In the last decade, Chk1 inhibitors have emerged as a novel therapeutic strategy to potentiate the anti-tumour efficacy of cytotoxic chemotherapeutic agents. In the search for new Chk1 inhibitors, a congeneric series of 2-aryl-2 <i>H</i>-pyrazolo[4,3-<i>c</i>]quinolin-3-one (PQ) was evaluated by <i>in-vitro</i> and <i>in-silico</i> approaches for the first time. A total of 30 PQ structures were synthesised in good to excellent yields using conventional or microwave heating, highlighting that 14 of them are new chemical entities. Noteworthy, in this preliminary study two compounds <b>4e<sub>2</sub></b> and <b>4h<sub>2</sub></b> have shown a modest but significant reduction in the basal activity of the Chk1 kinase. Starting from these preliminary results, we have designed the second generation of analogous in this class and further studies are in progress in our laboratories.</p
Deciphering the Complexity of Ligand–Protein Recognition Pathways Using Supervised Molecular Dynamics (SuMD) Simulations
Molecular
recognition is a crucial issue when aiming to interpret
the mechanism of known active substances as well as to develop novel
active candidates. Unfortunately, simulating the binding process is
still a challenging task because it requires classical MD experiments
in a long microsecond time scale that are affordable only with a high-level
computational capacity. In order to overcome this limiting factor,
we have recently implemented an alternative MD approach, named supervised
molecular dynamics (SuMD), and successfully applied it to G protein-coupled
receptors (GPCRs). SuMD enables the investigation of ligand–receptor
binding events independently from the starting position, chemical
structure of the ligand, and also from its receptor binding affinity.
In this article, we present an extension of the SuMD application domain
including different types of proteins in comparison with GPCRs. In
particular, we have deeply analyzed the ligand–protein recognition
pathways of six different case studies that we grouped into two different
classes: globular and membrane proteins. Moreover, we introduce the
SuMD-Analyzer tool that we have specifically implemented to help the
user in the analysis of the SuMD trajectories. Finally, we emphasize
the limit of the SuMD applicability domain as well as its strengths
in analyzing the complexity of ligand–protein recognition pathways
Novel 3‑Substituted 7‑Phenylpyrrolo[3,2‑<i>f</i>]quinolin-9(6<i>H</i>)‑ones as Single Entities with Multitarget Antiproliferative Activity
A series of chemically modified 7-phenylpyrroloÂ[3,2-<i>f</i>]Âquinolinones was synthesized and evaluated as anticancer
agents.
Among them, the most cytotoxic (subnanomolar GI<sub>50</sub> values)
amidic derivative <b>5f</b> was shown to act as an inhibitor
of tubulin polymerization (IC<sub>50</sub>, 0.99 ÎĽM) by binding
to the colchicine site with high affinity. Moreover, <b>5f</b> induced cell cycle arrest in the G2/M phase of the cell cycle in
a concentration dependent manner, followed by caspase-dependent apoptotic
cell death. Compound <b>5f</b> also showed lower toxicity in
nontumoral cells, suggesting selectivity toward cancer cells. Additional
experiments revealed that <b>5f</b> inhibited the enzymatic
activity of multiple kinases, including AURKA, FLT3, GSK3A, MAP3K,
MEK, RSK2, RSK4, PLK4, ULK1, and JAK1. Computational studies showed
that <b>5f</b> can be properly accommodated in the colchicine
binding site of tubulin as well as in the ATP binding clefts of all
examined kinases. Our data indicate that the excellent antiproliferative
profile of <b>5f</b> may be derived from its interactions with
multiple cellular targets