Molecular Dynamics Simulation

Background Thyroid receptors, TRα and TRβ, are involved in important physiological functions such as metabolism, cholesterol level and heart activities. Whereas metabolism increase and cholesterol level lowering could be achieved by TRβ isoform activation, TRα activation affects heart rates. Therefore, β-selective thyromimetics have been developed as promising drug-candidates for treatment of obesity and elevated cholesterol level. GC-1 [3,5-dimethyl-4-(4'-hydroxy-3'-isopropylbenzyl)-phenoxy acetic acid] has ability to lower LDL cholesterol with 600- to 1400-fold more potency and approximately two- to threefold more efficacy than atorvastatin (Lipitor©) in studies in rats, mice and monkeys. Results To investigate GC-1 specificity, we solved crystal structures and performed molecular dynamics simulations of both isoforms complexed with GC-1. Crystal structures reveal that, in TRα Arg228 is observed in multiple conformations, an effect triggered by the differences in the inter...

Computational methods and artificial intelligence became realistic and affordable to accelerate the identification of effective treatment against SARS-CoV-2. The host-pathogen interactome analyzed was used to identify hub drug targets, which are NSP16-NSP10 and NSP15. Here we screened some natural peptides against NSP15 and NSP10-NSP16 by utilizing molecular docking. Further, we developed a machine learning model and trained neural network, SVM, AdaBoost, Random Forest and kNN algorithms. In the next step, molecular dynamics simulation and MMPBSA employed. Assessment of these models was based on R², and the neural network was the best model (R² = 0.987), which was selected to predict the pIC 50 of chosen peptides. Therefore, we assessed the pharmacokinetic properties of the peptides with the highest pIC50 through in-silico ADME calculations. Jaspamide passed successfully through docking, ML predictions and ADME filtration and was subjected to molecular dynamics simulation and MMPBSA, which are commonly performed to investigate the stability of protein-drug complexes; therefore, we ran them to examine the stability of complexed jaspamide with both NSP15 and NSP10-NSP16. Network pharmacology showed that jaspamide has two antiviral mechanisms: SARS-CoV-2 activates/modulates innate and adaptive immune responses through IFN-stimulated genes and SARS-CoV-2-host interactions. These computational findings suggest that jaspamide merits experimental evaluation as a potential dual inhibitor of NSP15 and NSP16, but in vitro and in vivo studies are needed to confirm in silico results.

Avian flu H5N1 remains an important world health concern due to its prevalence in poultry farming and mortality rate among humans. Its impact has been worsened by its resistance to inhibitors such as oseltamivir and peramivir. In this chapter, we explore the potential of natural compounds from Indonesian medicinal plants such as Garcinia mangostana, Eurycoma longifolia, Brucea javanica, and Momordica charantia as new neuraminidase inhibitors through molecular docking. Using the blind docking method on Galaxy, we determine the binding affinities of major phytoconstituents to H5N1 neuraminidase. The study found that gamma-mangostin from G. mangostana and Kuguacin J from M. charantia had greater predicted binding affinities compared to other reference compounds. Although the study is limited as it is done in silico, it has provided an understanding of the potential of natural compounds from Indonesian medicinal plants as an alternative to known antivirals.

G-protein coupled receptors (GPCRs) belong to biologically important and functionally diverse and largest super family of membrane proteins. GPCRs retain a characteristic membrane topology of seven alpha helices with three intracellular, three extracellular loops and flanking N' and C' terminal residues. Subtle differences do exist in the helix boundaries (TM-domain), loop lengths, sequence features such as conserved motifs, amino acid patterns and their physiochemical properties amongst these sequences (clusters) at intra-genomic and inter-genomic level. In the current study, we employ prediction of helix boundaries and scores derived from amino acid substitution exchange matrices to identify the conserved amino acid residues (motifs) as consensus in aligned set of homologous GPCR sequences. Co-clustered GPCRs from human and other genomes, organized as 32 clusters, were employed to study the amino acid conservation patterns and species-specific or cluster-specific motifs. Critical analysis on sequence composition and properties provide clues to connect functional relevance within and across genome for vast practical applications such as design of mutations and understanding of disease-causing genetic abnormalities.

Excitatory amino acid transporters (EAATs) are membrane proteins responsible for reuptake of glutamate from the synaptic cleft to terminate neurotransmission and help prevent neurotoxically high, extracellular glutamate concentrations. Important structural information about these proteins emerged from crystal structures of GltPh, a bacterial homologue of EAATs, in conformations facing outward and inward. These remarkably different conformations are considered to be end points of the substrate translocation path (STP), suggesting that the transport mechanism involves major conformational rearrangements that remain uncharted. To investigate possible steps in the structural transitions of the STP between the two end-point conformations, we applied a combination of computational modeling methods (motion planning, molecular dynamics simulations, and mixed elastic network models). We found that the conformational changes in the transition involve mainly the repositioning the "transport domain" and the "trimerization domain" identified previously in the crystal structures. The two domains move in opposite directions along the membrane normal, and the transport domain also tilts by ∼17°with respect to this axis. Moreover, the TM3-4 loop undergoes a flexible, "restraining bar"-like conformational change with respect to the transport domain. As a consequence of these conformational rearrangements along the transition path we calculated a significant decrease of nearly 20% in the area of the transport-to-trimerization domain interface (TTDI). Water penetrates parts of the TTDI in the modeled intermediates but very much less in the end-point conformations. We show that these characteristics of the modeled intermediate states agree with experimental results from residue-accessibility studies in individual monomers and identify specific residues that can be used to test the proposed STP. Moreover, MD simulations of complete GltPh trimers constructed from initially identical monomer intermediates suggest that asymmetry can appear in the trimer, consonant with available experimental data showing independent transport kinetics by individual monomers in the trimers.

The membrane environment, its composition, dynamics, and remodeling, have been shown to participate in the function and organization of a wide variety of transmembrane (TM) proteins, making it necessary to study the molecular mechanisms of such proteins in the context of their membrane settings. We review some recent conceptual advances enabling such studies, and corresponding computational models and tools designed to facilitate the concerted experimental and computational investigation of protein-membrane interactions. To connect productively with the high resolution achieved by cognate experimental approaches, the computational methods must offer quantitative data at an atomistically detailed level. We show how such a quantitative method illuminated the mechanistic importance of a structural characteristic of multihelical TM proteins, that is, the likely presence of adjacent polar and hydrophobic residues at the protein-membrane interface. Such adjacency can preclude the complete alleviation of the well-known hydrophobic mismatch between TM proteins and the surrounding membrane, giving rise to an energy cost of residual hydrophobic mismatch. The energy cost and biophysical formulation of hydrophobic mismatch and residual hydrophobic mismatch are reviewed in the context of their mechanistic role in the function of prototypical members of multihelical TM protein families: 1), LeuT, a bacterial homolog of mammalian neurotransmitter sodium symporters; and 2), rhodopsin and the b1and b2-adrenergic receptors from the G-protein coupled receptor family. The type of computational analysis provided by these examples is poised to translate the rapidly growing structural data for the many TM protein families that are of great importance to cell function into ever more incisive insights into mechanisms driven by protein-ligand and protein-protein interactions in the membrane environment.

We present the dynamic mechanism of concerted motions in a full-length molecular model of the human dopamine transporter (hDAT), a member of the neurotransmitter/sodium symporter (NSS) family, involved in state-to-state transitions underlying function. The findings result from an analysis of unbiased atomistic molecular dynamics simulation trajectories (totaling >14 μs) of the hDAT molecule immersed in lipid membrane environments with or without phosphatidylinositol 4,5-biphosphate (PIP 2 ) lipids. The N-terminal region of hDAT (N-term) is shown to have an essential mechanistic role in correlated rearrangements of specific structural motifs relevant to state-to-state transitions in the hDAT. The mechanism involves PIP 2 -mediated electrostatic interactions between the N-term and the intracellular loops of the transporter molecule. Quantitative analyses of collective motions in the trajectories reveal that these interactions correlate with the inward-opening dynamics of hDAT and are allosterically coupled to the known functional sites of the transporter. The observed large-scale motions are enabled by specific reconfiguration of the network of ionic interactions at the intracellular end of the protein. The isomerization to the inward-facing state in hDAT is accompanied by concomitant movements in the extracellular vestibule and results in the release of an Na + ion from the Na2 site and destabilization of the substrate dopamine in the primary substrate binding S1 site. The dynamic mechanism emerging from the findings highlights the involvement of the PIP 2 -regulated interactions between the N-term and the intracellular loop 4 in the functionally relevant conformational transitions that are also similar to those found to underlie state-to-state transitions in the leucine transporter (LeuT), a prototypical bacterial homologue of the NSS.

Glycogen phosphorylase is a molecular target for the design of potential hypoglycemic agents. Structure‐based design pinpointed that the 3′‐position of glucopyranose equipped with a suitable group has the potential to form interactions with enzyme’s cofactor, pyridoxal 5′‐phosphate (PLP), thus enhancing the inhibitory potency. Hence, we have investigated the binding of two ligands, 1‐(β‐d‐glucopyranosyl)5‐fluorouracil (GlcFU) and its 3′‐CH2OH glucopyranose derivative. Both ligands were found to be low micromolar inhibitors with Ki values of 7.9 and 27.1 μm, respectively. X‐ray crystallography revealed that the 3′‐CH2OH glucopyranose substituent is indeed involved in additional molecular interactions with the PLP γ‐phosphate compared with GlcFU. However, it is 3.4 times less potent. To elucidate this discovery, docking followed by postdocking Quantum Mechanics/Molecular Mechanics – Poisson–Boltzmann Surface Area (QM/MM‐PBSA) binding affinity calculations were performed. While the doc...

Though used widely in cancer therapy, paclitaxel only elicits a response in a fraction of patients. A strong determinant of paclitaxel tumor response is the state of microtubule dynamic instability. However, whether the manipulation of this physiological process can be controlled to enhance paclitaxel response has not been tested. Here, we show a previously unrecognized role of the microtubule-associated protein CRMP2 in inducing microtubule bundling through its carboxy terminus. This activity is significantly decreased when the FER tyrosine kinase phosphorylates CRMP2 at Y479 and Y499. The crystal structures of wild-type CRMP2 and CRMP2-Y479E reveal how mimicking phosphorylation prevents tetramerization of CRMP2. Depletion of FER or reducing its catalytic activity using sub-therapeutic doses of inhibitors increases paclitaxel-induced microtubule stability and cytotoxicity in ovarian cancer cells and in vivo. This work provides a rationale for inhibiting FER-mediated CRMP2 phosphory...

Carbon Nanotubes (CNTs) have been used as the systems in drug delivery due to their exceptional physical and chemical properties. In this study, the adsorption of an anticancer drug Dacarbazine (DAC) into the inner and outer surface of pristine and Functionalized Carbon Nanotubes (FCNTs) with four carboxylic acid groups was investigated in aqueous solution using the Molecular Dynamics (MD) simulations. Our simulation results showed that in spite of the adsorption of drug molecules on the outer sidewall of pristine and functionalized nanotubes, the spontaneous encapsulation of DAC molecule into the cavity of CNTs and FCNTs is observed. The simulations show that the arrangement of the DAC molecule into the CNTs and FCNTs is controlled by p-p interactions.

Metal-organic frameworks (MOFs) are utilized as nanocarriers to enhance the efficiency of chemotherapy drugs, including cisplatin, which exhibit limitations such as side effects and resistance mechanisms. To evaluate the role of MOFs, we employed a molecular dynamics simulation, which, unlike other experiments, is cost-effective, less dangerous, and provides accurate results. Furthermore, we conducted molecular docking simulations to understand the interaction between cisplatin and MOF, as well as their internal interactions and how they bind to each other. Cisplatin and MOF molecules were parametrized using the Avogadro software and x2top command in GROMACS 5.1.2 and optimized by CP2K software; the Charmm-GUI site parametrized the cell cancer membrane. Three molecular dynamics simulations were conducted in four stages at various pHs, followed by simulated umbrella sampling. The simulations analyzed the pH responsiveness, total energy, Gibbs free energy, gyration radius, radial distribution function (RDF), solvent accessible surface area, and nanoparticles' toxicity. Results demonstrated that a neutral pH level (7.4) has greater adsorption and interaction compared to acidic pH values (6.4 and 5.4) because it displays the highest total energy (-17.1 kJ/mol), the highest RDF value (6.66), and the shortest distance (0.51 nm). Furthermore, the combination of cisplatin and MOFs displayed increased penetration compared to that of their individual forms. This study highlights the suitability of MOFs as nanocarriers and identifies the optimal pH values for desirable outcomes. Thus, it provides future studies with appropriate data to conduct their experiments in assessing MOFs.

Background: ␣-Conotoxin AuIB interacts with ␣3␤4 nAChRs and GABA B receptors, but structural determinants of these interactions are unknown. Results: Using alanine scanning mutagenesis and molecular dynamics, we identified residues crucial for AuIB⅐␣3␤4 nAChR interaction. We identified the key residues that mediate AuIB⅐␣3␤4 nAChR interaction. Significance: Ability to direct ␣-conotoxin binding to nAChRs or GABA B receptors will improve analgesic conopeptides.

Objective: Thymidylate Kinase (TMK) plays a crucial role in bacterial DNA synthesis by catalyzing the phosphorylation of Deoxythymidine Monophosphate (dTMP) to form Deoxythymidine Diphosphate (dTDP). Consequently, this enzyme emerges as a promising target for developing novel anti-cancer drugs. However, no anti-cancer drugs have been reported for this target until now. Methods: Ligands obtained from Benzylidene derivatives were examined for their potency by using molecular docking by glide module, Qikprop screening of Absorption, Distribution, Metabolism, and Excretion (ADME) study, and prime Molecular Mechanics in Generalized Bond Surface Area study (MM-GBSA) by binding free energy. Hereafter, a Molecular Dynamic (MD) simulation was performed at 100 ns to assess the stability of the potential ligand as a Human TMK (HaTMK) inhibitor. Results: These ten molecules showed good binding affinity and hydrogen and hydrophobic bond interactions with Arg150, Phe42, and Phe72 in the HaTMK enzyme (PDB id: 1E2D). Among them, trichloro-6-(((4-hydroxyphenyl)imino)methyl)phenol molecule had a high XP-docking score of (-7.87 kcal/mol), based on extra-precision data. Prime MM-GBSA studies also showed promising binding affinities i.e., ΔBind (-34.59 kcal/mol), ΔLipo (-13.92 kcal/mol), and ΔVdW (-34.42 kcal/mol). Arg76 and Phe72 residues maintained constant interactions with the ligand during Molecular Dynamics (MD) simulation. This ligand showed a potential binding affinity for the TMK target. Conclusion: The trichloro-6-(((4-hydroxyphenyl)imino)methyl)phenol ligand has active sites, namely benzene ring, benzylidene, and oxygen group, which actively participate in interaction with the protein of HaTMK, thus indicating good potential activity as the inhibitor of HaTMK to treat colon cancer.

Objective: This study explores the interactions of phenoxy acetamide derivatives with AMP-activated protein kinase (AMPK), a key enzyme in metabolic regulation. The goal is to evaluate the AMPK activation potential of these compounds using in silico approaches. Methods: Molecular docking was performed using the Glide module to assess binding affinity. Binding free energy (ΔG_bind) was calculated using the MM-GBSA method, and pharmacokinetic profiles were evaluated via ADME predictions using QikProp. Results: Among the tested compounds, 3-chlorophenyl phenoxy acetamide (compound 5) exhibited the highest XP-docking score of-5.22 kcal/mol and a ΔG_bind of-97.78 kcal/mol, indicating strong binding with the AMPK active site. Key interactions included hydrogen bonding with residues PRO127, MET84, ARG117, and TYR120. ADME analysis revealed that all compounds showed low CNS penetration (QPlog BB<-1) and acceptable intestinal absorption (Caco-2>300 nm/s). Conclusion: Compound 5 demonstrates significant AMPK activation potential and favorable ADME properties, suggesting its promise as a lead compound for type II diabetes therapy.

Objective: Thymidylate kinase (TMK) is pivotal in bacterial DNA synthesis, facilitating the conversion of Deoxythymidine Monophosphate (dTMP) into Deoxythymidine Diphosphate (dTDP). This crucial role positions TMK as an attractive target for the creation of innovative anti-cancer therapies. To date, there have been no anti-cancer medications developed specifically targeting this enzyme. Methods: The investigation involved screening benzylidene derivatives as potential ligands for their efficacy. This process was executed through the utilization of the Glide module for molecular docking, followed by an Absorption, Distribution, Metabolism, and Excretion (ADME) analysis via Qikprop. Subsequently, the Prime Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) approach was employed to evaluate the binding free energy of these ligands. To further assess the stability of these ligands as inhibitors of Human Thymidylate Kinase (HaTMK), molecular dynamics (MD) simulations were conducted over a 100 nanosecond timeframe. Results: Among the screened molecules, ten exhibited significant binding affinity, engaging in hydrogen and hydrophobic interactions with the Asp15, Phe105, and Phe72 residues of the HaTMK enzyme (PDB ID: 1E2D). Notably, the molecule 4-((4-dichlorobenzylidene) amino) phenol demonstrated the highest docking score with an Extra Precision (XP)-docking value of-6.33 kcal/mol, indicating a strong binding affinity based on extra-precision docking. Further analysis through Prime MM-GBSA revealed notable binding energies, including a ΔGBind of-52.98 kcal/mol, ΔGLipo of-27.75 kcal/mol, and ΔGVdW of-47.70kcal/mol, suggesting significant interaction strength. Throughout the MD simulations, interactions between the ligand and the Glu152 and Phe105 residues remained stable, underlining the molecule's potential as a TMK inhibitor. Conclusion: The ligand 4-((4-dichlorobenzylidene) amino)phenol, characterized by its benzene ring, benzylidene moiety, and oxygen group, engages effectively with the HaTMK protein's active sites. This interaction showcases its promising potential as an inhibitor of HaTMK, positioning it as a viable candidate for the treatment of colon cancer.

Time-dependent fluorescence shift (TDFS) of Laurdan embedded in phospholipid bilayers reports on hydration and mobility of the phospholipid acylgroups. Exchange of H2O with D2O prolongs the lifetime of lipid-water and lipid-water-lipid interactions, which is reflected in a significantly slower TDFS kinetics. Combining TDFS measurements in H2O and D2O hydrated bilayers with atomistic molecular dynamics (MD) simulations provides a unique tool for characterization of the hydrogen bonding at the acylgroup level of lipid bilayers. In this work, we use this approach to study the influence of fluoride anions on the properties of cationic bilayers composed of trimethylammonium-propane (DOTAP). The results obtained for DOTAP are confronted with those for neutral phosphatidylcholine (DOPC) bilayers. Both in DOTAP and DOPC H2O/D2O exchange prolongs hydrogen-bonding lifetime and does not disturb bilayer structure. These results are confirmed by MD simulations. TDFS experiments show, however, th...

The behavior of oxysterols in phospholipid membranes and their effects on membrane properties was investigated by means of dynamic light scattering, fluorescence spectroscopy, NMR, and extensive atomistic simulations. Two families of oxysterols were scrutinizedtail-oxidized sterols, which are mostly produced by enzymatic processes, and ring-oxidized sterols, formed mostly via reactions with free radicals. The former family of sterols was found to behave similarly to cholesterol in terms of molecular orientation, roughly parallel to the bilayer normal, leading to increasing membrane stiffness and suppression of its membrane permeability. In contrast, ringoxidized sterols behave quantitatively differently from cholesterol. They acquire tilted orientations and therefore disrupt the bilayer structure with potential implications for signaling and other biochemical processes in the membranes.