ARTICLE | doi:10.20944/preprints202309.1739.v1
Subject: Chemistry And Materials Science, Physical Chemistry Keywords: pressure temperature; ZnO; MD; Chemical Bonds
Online: 27 September 2023 (02:29:58 CEST)
Zinc oxide (ZnO) as a semiconductor in its crystalline or amorphous form is still a promised material, especially under isobaric and isothermal ensembles. In this work, Parallel and Equilibrium Molecular Dynamics and DL_POLY_4 software are employed to predict the relationship between the behavior of ZnO chemical bonds and the phase transition literatures, using correlation function g(r) of Zn-Zn, Zn-O, and O-O pairs. Our system is composed of 5832 atoms of ZnO rocksalt structure (2916 atoms of Zn2+ and 2916 atoms of O2-), under the temperature of 300 (K) and the range of pressure 0-400 (GPa). The lengths of ZnO bonds, the standard error, standard deviation, the maximum of g(r), and the percentage of the variation of the bonds are analyzed. The interatomic interactions are modeled by the potential of Buckingham for short-range and Coulomb for long-range interactions. The calculations were run on the RAVEN Supercomputer of Cardiff University (UK). Our data are mostly in the vicinity of available information of bonds lengths; the rest can be deduced from the pressure of phase transition to use it as a new approach of phase transition confirmation. However, the rest of our results are still a prediction because of no results under extended pressure used in this work.
ARTICLE | doi:10.20944/preprints202302.0282.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: PTEN; SHIP2; C2 domain; Ptase domain; MD
Online: 16 February 2023 (09:22:30 CET)
Phosphatase and tensin homologue (PTEN) and SH2-containing-inositol-5’-phosphatase 2 (SHIP2) are structurally and functionally similar. They both consist of a Phosphastase (Ptase) domain and an adjacent C2 domain, and both proteins dephosphorylate phosphoinositol-tri(3,4,5)phosphate, PI(3,4,5)P3; PTEN at the 3-phophate and SHIP2 at the 5-phosphate. Therefore, they play pivotal roles in the PI3K/Akt pathway. Here, we investigate the role of the C2 domain in membrane interactions of PTEN and SHIP2, using molecular dynamics simulations and free energy calculations. It is generally accepted that for PTEN the C2 domain interacts strongly with anionic lipids and therefore significantly contributes to membrane recruitment. In contrast, for the C2 domain in SHIP2 we previously found much weaker binding affinity for anionic membranes. Our simulations confirm the membrane anchor role of the C2 domain in PTEN, as well as its necessity for the Ptase domain in gaining its productive membrane binding conformation. In contrast, we identified that the C2 domain in SHIP2 undertakes neither of these roles, which are generally proposed for C2 domains. Our data support a model in which the main role of the C2 domain in SHIP2 is to introduce allosteric interdomain changes that enhance catalytic activity of the Ptase domain.
ARTICLE | doi:10.20944/preprints202310.1802.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: diabetes; terpenes; docking; MD simulation; MM-GBSA; DFT
Online: 27 October 2023 (11:50:06 CEST)
African indigenous herbs and medicinal plants are extensively reported for their protective and therapeutic potential against Diabetes. However, most of the constituent phytochemicals that may account for the therapeutic activity are largely uninvestigated. Exploring novel phytochemical–target interactions in silico could help to provide useful insights into the mechanism underpinning the biological activities of these plants and their constituent phytochemicals. The aim of this study was to explore the interactions of terpene struc-tures previously reported from selected African antidiabetic with two emerging drug targets in diabetes. Structure-based virtual screening was used to screen 107 terpene structures against DPP-4 and PTP1B enzymes. The MD simulation, MM-GBSA free energy calculation and DFT were used to clarify the inter-actions of the in silico hits with the target enzymes. Molecular docking, post-docking Prime MM-GBSA analysis revealed the top terpenes with high binding affinity with the active site regions of DPP-4 and PTP1B. Ensemble docking revealed three triterpenes viz: cucurbitacin B (T1), 6-Oxoisoiguesterin (T4) and 20-Epi-isoiguesterinol (T2) as in silico hits which exhibit strong interaction potential with critical residues that define the catalytic triad (Ser630 and His740); oxyanion cavity (Ser631); hydrophobic S1 pocket (Tyr662) and the charged S2 pocket (Arg125) in the active site region of DPP-4. The interactions of these compounds with DPP-4 exhibited structural stability and conformational flexibility during 100 ns full atomistic MD simulation as indicated by the structure dynamics parameters including RMSD, RoG, SASA and hydrogen bond number. The post-MD MM/GBSA calculations further revealed the stability of the triterpene-DPP-4 complexes. Furthermore, Frontier molecular orbital calculations showed that, the triterpenes possess high interaction potential with the enzyme. The triterpenes showed desirable ADMET properties and drug-likeness. Therefore, cucurbitacin B, 6-Oxoisoiguesterin and 20-Epi-isoiguesterinol are recommended for experimental validation.
ARTICLE | doi:10.20944/preprints201908.0238.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: aurora kinase A; molecular docking; DFT; MD simulation
Online: 23 August 2019 (05:01:40 CEST)
Aurora kinase A (AURKA) is a normal cell proliferation-inducing enzyme encoded by AURKA gene, with over-expression observed in different types of malignancies. Hence, the goal is to find potential inhibitors against AURKA. In this study, molecular docking, Standard Precision and Extra Precision methods were employed. After the docking study, the ligands showed an extremely low binding score which suggested very high binding affinity of the ligands. Furthermore, Quantum polarized ligand docking (QPLD) was performed to predict the binding status of the molecules. Based on the binding affinity, the top four compounds were chosen for further analysis. The docked complexes were further analyzed in explicit water conditions using 100 ns molecular dynamics simulations and binding free energy calculation. Then, density functional theory (DFT) calculation was used to calculate the molecular properties of the molecules. Finally, systems biology experiments validated the molecular docking and molecular dynamics simulation studies and indicated that quercetin, kaempferol, luteolin and rutin could inhibit the AURKA. The results show that, these four molecules have high binding affinity to the AURKA and significant interactions (LEU139, GLU211and ALA213) were also identified with the hinge region of Aurora kinase A. Thus, LEU139, GLU211, and ALA213 were identified as the crucial protein mechanisms.
ARTICLE | doi:10.20944/preprints202302.0059.v1
Subject: Biology And Life Sciences, Biophysics Keywords: hSERT; comprehensive molecular dynamics (MD) simulation; drug design; MM/GBSA
Online: 3 February 2023 (06:16:06 CET)
The human serotonin transporter (hSERT) terminates neurotransmission by removing serotonin from the synaptic cleft, which is an essential process plays an important role in depression. In addition to substrate serotonin, hSERT is also the target of drugs of abuse like cocaine and clinically used antidepressants such as escitalopram and paroxetine. To date, few studies attempt to investigate the unbinding mechanism underlying the orthosteric and allosteric modulation of hSERT. The high-resolution X-ray structure of hSERT resolved recently enables us to theoretically study the unbinding of the above four ligands against the S1 or S2 site of hSERT, by means of molecular docking, molecular dynamics (MD) and potential of mean force (PMF) simulations. We proved that for either the S1 or S2 site, the other three ligands (cocaine, escitalopram and paroxetine) are much more favorable than the original substrate serotonin, whether in kinetics along the unbinding pathways or in thermodynamics at the equilibrium states. Furthermore, the S1 site is much more favorable than the S2 site, for each ligand. Interestingly, inspection revealed that there are ~ 3Å lengths between the allosteric site of serotonin and cocaine, and an unseen un-binding pathway for escitalopram at the S1 site except for verification of the broadest trail.
ARTICLE | doi:10.20944/preprints202301.0260.v1
Subject: Chemistry And Materials Science, Physical Chemistry Keywords: host-guest inclusion strategy; pyrolysis decomposition; ReaxFF-MD; reaction rate
Online: 16 January 2023 (02:17:12 CET)
The host-guest inclusion strategy has potential to surpass the limitations of energy density and suboptimal performances of single explosives. The guest molecules can not only enhance the detonation performance of host explosives but can also enhance their stability. Therefore, the deeply analysis the role of guest influence on the pyrolysis decomposition of the host-guest explosive is necessary. The whole decomposition reaction stage of CL-20/H2O, CL-20/CO2, CL-20/N2O, CL-20/NH2OH was calculated by ReaxFF-MD. The incorporation of CO2, N2O and NH2OH significantly increase the energy levels of CL-20. However, different guest has little influence on the initial decomposition paths of CL-20. The Ea1 and Ea2 values of CL-20/CO2, CL-20/N2O, CL-20/NH2OH systems are higher than the CL-20/H2O system. Clearly, incorporation of CO2, N2O, NH2OH can inhibit the initial decomposition and intermediate decomposition stage of CL-20/H2O. Guest molecules get heavily involved in the reaction and influence on the reaction rate. k1 of CL-20/N2O and CL-20/NH2OH systems are significantly larger than that of CL-20/H2O at high temperatures. k1 of CL-20/CO2 system is much complex, which can be affected deeply by temperatures. k2 of CL-20/CO2, CL-20/N2O system is significantly smaller than that of CL-20/H2O at high temperatures. k2 of CL-20/NH2OH system is little difference at high temperatures. For the CL-20/CO2 system, the k3 value of CO2 is slight higher than that for CL-20/H2O, CL-20/N2O, CL-20/NH2OH systems, while the k3 values of N2 and H2O are slight smaller than that for CL-20/H2O, CL-20/N2O, CL-20/NH2OH systems. For the CL-20/N2O system, the k3 value of CO2 is slight smaller than that for CL-20/H2O, CL-20/CO2, CL-20/NH2OH systems. For the CL-20/NH2OH system, the k3 value of H2O is slight larger than that for CL-20/H2O, CL-20/CO2, CL-20/N2O systems. These mechanisms revealed that CO2, N2O and NH2OH molecules inhibit the early stages of the initial decomposition of CL-20, and play an important role for the decomposition subsequently.
ARTICLE | doi:10.20944/preprints202206.0348.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Naltrexone; mu-opioid receptor; MD simulations; MMGBSA; binding free energy
Online: 27 June 2022 (04:09:30 CEST)
Naltrexone (NTX) is a potent opioid antagonist with good blood-brain barrier permeability, targeting different endogenous opioid receptors, particularly the mu-opioid receptor (MOR). Therefore, it represents a promising candidate for drug development against drug addiction. However, the details of the molecular interactions of NTX and its derivatives with MOR are not fully understood, hindering ligand-based drug discovery. In the present study, taking advantage of the high-resolution X-ray crystal structure of the murine MOR (mMOR), we constructed a homology model of the human MOR (hMOR). A solvated phospholipid bilayer was built around the hMOR and submitted to microsecond (µs) molecular dynamics (MD) simulations to obtain an optimized hMOR model. NTX and its derivatives were docked into the optimized hMOR model and submitted to µs MD simulations in an aqueous membrane system. The MD simulation results were submitted to Molecular Mechanics Generalized-Born surface area (MMGBSA) binding free energy calculations and principal component analysis. Our results revealed that NTX and its derivatives showed differences in protein-ligand interactions; however, they shared contact with residues at TM2, TM3, H6, and TM7. The binding free energy and principal component analysis revealed the structural and energetic effects responsible for the higher potency of NTX compared to its derivatives.
ARTICLE | doi:10.20944/preprints202107.0039.v1
Subject: Biology And Life Sciences, Biophysics Keywords: Mixed-chain lipids; Neutron scattering; X-ray scattering; MD simulations
Online: 1 July 2021 (22:26:58 CEST)
We addressed the frequent occurrence of mixed-chain lipids in biological membranes and their impact on membrane structure by studying several chain-asymmetric phosphatidylcholines and the highly asymmetric milk sphingomyelin. Specifically, we report trans-membrane structures of the corresponding fluid lamellar phases using small-angle X-ray and neutron scattering, which were jointly analyzed in terms of a membrane composition-specific model, including a headgroup hydration shell. Focusing on terminal methyl groups at the bilayer center we found a linear relation between hydrocarbon chain length mismatch and the methyl-overlap for phosphatidylcholines, and a non-negligible impact of the glycerol backbone-tilting, letting the sn1-chain penetrate deeper into the opposing leaflet by half a CH2 group. That is, penetration-depth differences due to the ester-linked hydrocarbons at the glycerol backbone, reported previously for gel phase structures also extend to the physiological more relevant fluid phase, but are significantly reduced. Moreover, milk sphingomyelin was found to follow the same linear relationship suggesting a similar tilt of the sphingosine backbone. Complementary performed molecular dynamics simulations revealed that there is always a part of the lipid tails bending back, even if there is a high interdigitation with the opposing chains. This suggests that hydrocarbon chain interdigitation plays only a minor role in transbilayer coupling. For both cases of adaption to chain length mismatch, chain-asymmetry has a large impact on hydrocarbon chain ordering, inducing disorder in the longer of the two hydrocarbons.
ARTICLE | doi:10.20944/preprints201808.0532.v1
Subject: Chemistry And Materials Science, Theoretical Chemistry Keywords: MDR transporters; MATE family; NorM; MD simulation; loops; sodium ions
Online: 30 August 2018 (14:43:53 CEST)
The multidrug resistance transporter NorM is an important drug resistance pump and plays a critical role in multidrug resistance in bacteria and mammals. In this study we carried out molecular dynamics simulation to study the mechanism of Na+ binding and dynamical structures of two long loops in the substrate-releasing process in substrate binding NorM. Our simulation study identified several key residues (D41, E261 D377) along the Na+ binding pathway and a multi-state ion-binding mechanism is proposed based on the simulation study. In this proposed model, the transport of Na+ is a multi-stage process with D41 being the first station for binding to Na+, followed by Na+ binding to the second station E262 and finally to the cation-binding site of E262 and D377. During the transport of Na+, the transmembrane components TM1, TM7 and TM2 are rearranged to facilitate the ion transport as well conformational changes of NorM to a closed state. Further, substrate-bound simulation revealed that Loop3-4 and Loop9-10 control the substrate-releasing process.
ARTICLE | doi:10.20944/preprints202308.0232.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Colon Cancer; Apoptosis; BMAP-27; Peptide therapy; Molecular Docking; MD-Simulation
Online: 2 August 2023 (13:22:18 CEST)
BMAP-27 peptide known to exert cytotoxic effects against cancer cells by membrane integrity disruption. In the current investigation, we aimed to study the role of the BMAP-27 peptide in reducing colon cancer cell proliferation and inducing apoptosis. This study utilized both primary and metastatic colon cancer cell lines (SW480 and SW620). Proliferation was measured using CCK-8, and cellular damage was analyzed by lactate dehydrogenase assay. The study assessed apoptosis, cell cycle, and proliferation by measuring the expression of CASPASE3, BAX, BCL-2, TP53, CDK-6, PCNA, Wnt11, AXIN1, and CTNNB1. Additionally, in-silico studies were conducted to determine the binding affinities of BMAP-27 with APC and β-catenin proteins. BMAP-27 peptide reduced colon cancer cell proliferation, upregulated CASPASE3, BAX, TP53, AXIN1 expression, and downregulated BCL-2, CDK-6, PCNA, WNT11, CTNNB1 in both colon cancer cell lines, however, demonstrated higher activity in primary than metastatic colon cancer cells. The molecular dynamic simulation revealed substantial binding affinity of the peptide to adenomatous polyposis coli and β-catenin proteins.BMAP-27 peptide effectively inhibited the proliferation and enhanced apoptosis in the primary than in metastatic colon cancer cells. In-silico findings suggest that BMAP-27 exhibits a strong binding affinity with APC and β-catenin, highlighting its potential role as an anti-colon cancer agent.
ARTICLE | doi:10.20944/preprints202112.0475.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: heme distortion; pocket rigidity; protein environment; hemoglobin; myoglobin; MD simulation; ONIOM
Online: 29 December 2021 (23:52:57 CET)
Heme is located in the active site of proteins and has diverse and important biological functions, such as electron transfer and oxygen transport and/or storage. The distortion of heme porphyrin is considered an important factor for the diverse functions of heme because it correlates with the physical properties of heme, such as oxygen affinity and redox potential. Therefore, clarification of the relationship between heme distortion and the protein environment is crucial in protein science. Here, we analyzed the fluctuation in heme distortion in the protein environment for hemoglobin and myoglobin using molecular dynamics (MD) simulations and quantum mechanical (QM) calculations. We also investigated the protein structures of hemoglobin and myoglobin stored in Protein Data Bank and found that heme is distorted along the doming mode, which correlates with its oxygen affinity, more prominently in the protein environment than in the isolated state, and the magnitude of distortion is different between hemoglobin and myoglobin. This tendency was also observed in the results of MD simulations and QM calculations. These results suggest that heme distortion is affected by its protein environment and fluctuates around its fitted conformation, leading to physical properties that are appropriate for protein functions.
ARTICLE | doi:10.20944/preprints202003.0466.v1
Subject: Medicine And Pharmacology, Pharmacology And Toxicology Keywords: COVID-19; SARS-CoV-2 RBD; Ubrogepant; ACE-2; MD simulation
Online: 31 March 2020 (22:50:27 CEST)
Background: COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global pandemic affecting approximately 490,000 people and accounting for more than 22,000 deaths and has no generally acceptable cure. Here, the recently resolved 3D structure of SARS-CoV-2 receptor binding domain (RBD) in complex with its receptor-the angiotensin converting enzyme-2 (ACE-2) have provided the basis for screening chemical database for novel entry inhibitors. Methods: Molecular docking protocols have been used to rapidly screen FDA database for high affinity interaction at the SARS-CoV-2-RBD/ACE-2 interface. One of the top candidates, ubrogepant has been selected and further studied using atomistic molecular dynamics simulation method. Results: Molecular docking result showed that ubrogepant (UBR) and darunavir have binding energies of -10.4 kcal/mol. MMPBSA free energy analyses of UBR bound to RBD, ACE-2 and RBD/ACE-2 revealed RBD/ACE-2 > ACE-2 > RBD preference. Network analysis showed that interaction captured in the crystal structure were disrupted in UBR-bound state, hydration of the interface and increased atomic fluctuation within the RBD oligomerization interface and ACE-2 zinc binding site. Conclusions: The ability of ubrogepant to rupture the interaction at the RBD/ACE-2 interface residues of SARS-CoV-2 RBD/ACE-2 complex may result in loss of protein function with direct implication on oligomerization formation in RBD and loss of function in ACE-2 thus, making binding, cellular receptor recognition impossible. General Significance: Ubrogepant represents a new therapeutic candidate in the fight against COVID-19, as it binds with relatively high affinity with free RBD, ACE-2 receptor and SARS-CoV-2 RBD/ACE-2 complex based on binding affinity calculations.
ARTICLE | doi:10.20944/preprints201811.0118.v1
Subject: Social Sciences, Sociology Keywords: Gentrification; Residential Migration; Black Middle Class; Washington, DC; PG County, MD
Online: 5 November 2018 (14:06:31 CET)
The implications of urban revitalization, gentrification, and residential migration have attracted widespread interest and ongoing debate among scholars across a range of disciplines. While a significant body of literature explores race and class interactions within urban gentrifying neighborhoods, few have examined the environments that await those displaced by this process. This study explores the social and political impact of urban gentrification and class stratification within the black community by examining responses of black middle class residents in Prince George’s County, MD to the growing in-migration of low-income and minority residents from Washington, DC. Drawing on data from the U.S. Census Bureau, a multi-neighborhood sample of ninety-five black middle class residents of Prince George’s County, and informal interviews with subject-area experts, this study explores how race and class shape residential decisions and their impact on residential mobility initiatives. Residents responded to a 26-item survey that covered demographic information, political and community engagement, and their attitudes and beliefs about the poor, changes in their community, and racial unity and responsibility. Findings from cross tabulations and binary logistic regression indicate that lower middle class residents are the most likely to resist in-migration by exiting their communities and/or voting against proposals to create affordable housing options. Core and upper middle class residents were the most likely to stay in their neighborhoods despite increases in low-income migration, to vote in support of policies to create affordable housing options and to believe their responsibility to poor blacks could include sharing residential space.
ARTICLE | doi:10.20944/preprints202102.0171.v1
Subject: Chemistry And Materials Science, Theoretical Chemistry Keywords: P–fertility, orthophosphate, glycerolphosphate, inositolhexaphosphate, goethite, adsorption, surface complexation, MD simulations, QMMM
Online: 8 February 2021 (07:43:53 CET)
Knowledge of the interaction between inorganic and organic phosphates with soil minerals is vital for improving the soil P fertility. To achieve an in-depth understanding we combined adsorption experiments and hybrid ab initio molecular dynamics simulations to analyze the adsorption of common phosphates, i.e. orthophosphate (OP), glycerolphosphate (GP) and inositolhexaphosphate (IHP), onto the 100 surface plane of goethite. Experimental adsorption data per mol P-molecule basis fitted to the Freundlich model show the adsorption strength increases in the order GP < OP < IHP, and IHP adsorption being saturated faster followed by GP and OP. Modeling results show that OP and GP form stable monodentate (M) and binuclear bidentate (B) motifs with B being more stable than M, whereas IHP forms stable M and 3M motifs. Interfacial water plays an important role through hydrogen bonds and proton transfers with OP/GP/IHP and goethite. It also controls the binding motifs of phosphates with goethite. Combining both experimental and modeling results, we propose that the B motif dominates for OP, whereas GP forms M and IHP forms a combination of M and 3M motifs. The joint approach plausibly explains why IHP is the predominant organically bound P form in soil. This study could be considered as a preliminary step for further studies for understanding the mechanisms of how microbes and plants overcome the strong IHP–mineral binding to implement the phosphate groups into their metabolism.
ARTICLE | doi:10.20944/preprints202303.0502.v1
Subject: Medicine And Pharmacology, Pharmacology And Toxicology Keywords: Tuberculosis; Biscoumarins; Ligand molecules; DprE1; Anti-tuberculosis activity; Molecular docking; MD Simulation; Cytotoxicity
Online: 29 March 2023 (04:21:45 CEST)
The concerning rise in emergence and prevalence of resistant strains to drugs of M. tuberculosis has ,the prompted researchers to look for new and effective treatments. With this motive, biscoumarins were identified as the lead molecules on a whole-cell-based screening of several less explored low molecular weight bioactive compounds against M. tuberculosis strains. Among the screened biscoumarins, the highest dock score derivatives were synthesized (a-h) using a programmable microwave synthesizer for better yields and reaction control. The synthesized derivatives were evaluated against H37Rv, H37Ra, M. smegmatis, an MDR surrogate model, and other bacterial strains for the structure-activity response. Assessment of the synthesized library against mycobacterial strains led to the identification of compounds (f and d) as lead anti-tuberculosis agents. Compounds (f and d) exhibited less toxicity against human cell lines. At the same time, it displayed enjoyable activity wherein MIC concentrations were observed to be 16- and 32 µg/mL against the susceptible H37Rv, and H37Ra strains of M. tuberculosis and MIC value of 128 µg/mL for M. smegmatis, respectively. For mechanistic insights and identification of drug binding targets, molecular docking and dynamic simulations were employed for a panel of 16 mycobacterial enzymes essential for mycobacterial growth and survival. These in silico studies revealed the DprE1 enzyme as a druggable target for the anti-tuberculosis activity of the selected biscoumarins derivatives. Further investigation is underway in our laboratory, leading to its development as an anti-tuberculosis drug (animal model studies).
REVIEW | doi:10.20944/preprints202307.0497.v1
Subject: Biology And Life Sciences, Life Sciences Keywords: food allergies; Mediterranean diet; MD; olive oil; polyphenols; long-chain omega-3 fatty acids
Online: 10 July 2023 (04:58:57 CEST)
Allergies are a common and increasing health problem affecting millions of people worldwide. In addition to genetic predisposition, this increase in allergic cases is attributed to air pollution, climate change, more time spent indoors, lack of physical activity, and alterations in eating habits. The Mediterranean diet (MD), which includes a lot of fruits and vegetables, whole grains, legumes, nuts, olive oil and fish has been linked to a variety of health benefits, including a lower risk of chronic and allergic diseases. The purpose of this paper is to explore the effects of the dietary components of the MD on food allergies. Electronic databases PubMed, Scopus, Science Direct, and EBSCO were used to conduct this systematic review up to March 2023. 696 studies were initially identified and nine were included (five human and four animal studies). The findings of this review showed an overall beneficial effect between the food components of the MD and food allergies. Although the results are promising, the limited number of studies highlights the need for more research.
REVIEW | doi:10.20944/preprints202202.0154.v1
Subject: Chemistry And Materials Science, Theoretical Chemistry Keywords: computational chemistry; fragment screening; MD; MIP; molecular dynamics; molecular imprinting; molecularly imprinted polymer; simulation; template
Online: 10 February 2022 (14:37:50 CET)
The past two decades have witnessed the introduction of and then a steady increase in the use of computational techniques in the study and development of molecularly imprinted polymers (MIPs). Molecular dynamics (MD) based studies have had a significant role in this development as they can provide insights concerning the mechanisms governing the molecular level events underlying MIP synthesis and MIP-ligand interactions and can be used for the identification of preferred monomer compositions and for the prediction of MIP properties. We here review the role that MD has played in the development of molecular imprinting and examine the different types of MD strategies that have been used, including their advantages and challenges. Recent trends in the application of MD to the study of MIPs are presented, along with a perspective on the future importance of MD-based studies for the development of molecular imprinting science and technology.
ARTICLE | doi:10.20944/preprints202105.0011.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Annocatacin B; ND1 Subunit; Mitochondrial Respiratory Complex I; MRC-I; Molecular Dynamics Simulations; MD; Hirshfeld Charges; MM/PBSA
Online: 3 May 2021 (16:13:49 CEST)
ND1 subunit possesses the majority of the inhibitor binding domain of the human MRC-I. This is an attractive target for the search for new inhibitors that seek mitochondrial dysfunction. It is known, from in vitro experiments, some metabolites from Annona muricata called acetogenins have important biological activities such as anticancer, antiparasitic, and insecticide. Previous studies propose an inhibitory activity of bovine MRC-I by bis-THF acetogenins such as annocatacin B, however, there are few studies on its inhibitory effect on human MRC-I. In this work, we evaluate the molecular and energetic affinity of the annocatacin B molecule with the human ND1 subunit in order to elucidate its potential capacity to be a good inhibitor of this subunit. For this purpose, QM optimizations, MD simulations and MM/PBSA analysis were performed. As a control to compare our outcomes, the molecule rotenone, which is a known MRC-I inhibitor, was chosen. Our results show that annocatacin B has a greater affinity for the ND1 structure, its size and folding were probably the main characteristics that contributed to stabilize the molecular complex. Furthermore, the MM/PBSA calculations showed a 35% stronger BFE compared to the rotenone complex. Detailed analysis of the BFE shows that the aliphatic chains of annocatacin B play a key role in molecular coupling by distributing favorable interactions throughout the major part of the ND1 structure. These results are consistent with experimental studies that mention that acetogenins may be good inhibitors of MRC-I.
ARTICLE | doi:10.20944/preprints201812.0336.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: complement factor H (CFH); molecular docking; molecular dynamics (MD) simulation; computational alanine scanning (CAS); experimental alanine scanning (EAS)
Online: 28 December 2018 (06:55:53 CET)
The details of antigen-antibody interactions and the identification of epitopes are critical for the development of monoclonal antibody drugs. Ab42 is a native human-derived anti-CFH monoclonal antibody. In this study, the interaction between antigen pCFH and antibody (Ab42) was theoretically demonstrated by molecular docking and MD simulation, combined with free energy calculation and computational alanine scanning (CAS), and key amino acids and epitopes were identified. Experimental alanine scanning (EAS) was then carried out to verify the results of the calculation, and our results indicated that Ab42 antibody forms hydrogen bonds and interacts hydrophobically with pCFH through the Tyr315, Ser100, Gly33, and Tyr53 residues on its CDR, while the main pCFH epitopes are located at the six sites of Pro441, Ile442, Asp443, Asn444, Ile447, and Thr448. In conclusion, this study has explored the mechanism of antigen-antibody interaction from both theoretical and experimental aspects, and our results have important theoretical significance for the design and development of relevant antibody drugs.
ARTICLE | doi:10.20944/preprints202008.0508.v1
Subject: Medicine And Pharmacology, Orthopedics And Sports Medicine Keywords: heart rate monitor; ECG; portable/wearable monitoring system; heart rate variability; long-term assessment; arrhythmia; QARDIO MD VSI system
Online: 24 August 2020 (07:45:40 CEST)
Heart Rate Monitors (HRMs) are an indispensable tool for controlling training parameters of healthy athletes. They became a source of information about stress heart rhythm disturbances, recognized as unexpected increases in heart rate (HR), which can be life-threatening for athletes. Most HRMs do not recognize the type of arrhythmia, confusing them with artifacts. The aim of the study was to assess the usefulness of ECG recording functions by sports HRMs among endurance athletes, coaches, and physicians in comparison with other basic and hypothetical functions. We conducted 3 surveys among endurance athletes (76 runners, 14 cyclists, and 10 triathletes), as well as 10 coaches and 10 sports doctors to obtain information on how important ECG recording is, and what functions of HRMs should be improved to meet their expectations in the future. The respondents were asked questions regarding use and hypothetical functions, as well as preference for HRM type (optical/strap). For athletes, the 4 most important functions were distance traveled, pace, instant heart rate, and information about reaching the oxygen threshold. ECG recording was the 8th and 9th most important for momentary and continuous, respectively. Coaches opined more importance to ECG recording. Doctors placed ECG recording as most important. All participants preferred optical HRMs to strap HRMs. Research on the improvement and implementation of HRM functions shows slightly different preferences of athletes compared to coaches and doctors. Suspected arrhythmia increases the value of the HRM’s ability to record ECGs during training by athletes and coaches. For doctors, this is the most desirable feature in any situation. Considering the expectations of all groups continuous ECG recording during training will significantly improve the safety of athletes.
Subject: Computer Science And Mathematics, Computer Vision And Graphics Keywords: Gaussian noise; Speckle Noise; Mean square error(MSE); DE noising filters; Maximum difference value (MD); Peak signal to noise ratio(PSNR)
Online: 4 June 2020 (05:52:55 CEST)
Noise reduction in medical images is a perplexing undertaking for the researchers in digital image processing. Noise generates maximum critical disturbances as well as touches the medical images quality, ultrasound images in the field of biomedical imaging. The image is normally considered as gathering of data and existence of noises degradation the image quality. It ought to be vital to reestablish the original image noises for accomplishing maximum data from images. Medical images are debased through noise through its transmission and procurement. Image with noise reduce the image contrast and resolution, thereby decreasing the diagnostic values of the medical image. This paper mainly focuses on Gaussian noise, Pepper noise, Uniform noise, Salt and Speckle noise. Different filtering techniques can be adapted for noise declining to improve the visual quality as well as reorganization of images. Here four types of noises have been undertaken and applied on medical images. Besides numerous filtering methods like Gaussian, median, mean and Weiner applied for noise reduction as well as estimate the performance of filter through the parameters like mean square error (MSE), peak signal to noise ratio (PSNR), Average difference value (AD) and Maximum difference value (MD) to diminish the noises without corrupting the medical image data.
REVIEW | doi:10.20944/preprints201811.0018.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Duchenne muscular dystrophy (DMD); CRISPR/Cas9; exon skipping therapy; gene editing; human induced pluripotent stem cells (hiPSCs); immortalized patient muscle cells; mdx mice; humanized dystrophic mouse models; deltaE50-MD dog model
Online: 2 November 2018 (05:14:23 CET)
Duchenne muscular dystrophy (DMD) is a fatal X-linked recessive neuromuscular disease prevalent in 1 in 3500 to 5000 males worldwide. As a result of mutations that interrupt the reading frame of the dystrophin gene (DMD), DMD is characterized by a loss of dystrophin protein which leads to decreased muscle membrane integrity, which increases susceptibility to degeneration. CRISPR/Cas9 technology has garnered interest as an avenue for DMD therapy due to its potential for permanent exon skipping, which can restore the disrupted DMD reading frame in DMD and lead to dystrophin restoration. An RNA-guided DNA endonuclease system, CRISPR/Cas9 allows for the targeted editing of specific sequences in the genome. The efficacy and safety of CRISPR/Cas9 as a therapy for DMD has been evaluated by numerous studies in vitro and in vivo, with varying rates of success. Despite the potential of CRISPR/Cas9-mediated gene editing for the long-term treatment of DMD, its translation into the clinic is currently challenged by issues such as off-targeting, immune response activation, and sub-optimal in vivo delivery. Its nature as being mostly a personalized form of therapy also limits applicability to DMD patients, who exhibit a wide spectrum of mutations. This review summarizes the various CRISPR/Cas9 strategies that have been tested in vitro and in vivo for the treatment of DMD. Perspectives on the approach will be provided, and the challenges faced by CRISPR/Cas9 in its road to the clinic will be briefly discussed.