NpT-ensemble Monte Carlo calculations for binary liquid mixtures

Unveiling the multitargeted potency of Sodium Danshensu against cervical cancer: a multitargeted docking-based, structural fingerprinting and molecular dynamics simulation study

Cervical Cancer (CC) is one of the most common types of cancer in women worldwide, with a significant number of deaths reported yearly. Despite the various treatment options available, the high mortality rate associated with CC highlights the need to develop new and effective therapeutic agents. In this study, we have screened the complete prepared FDA library against the Mitotic kinesin-like protein 1, Cyclin B1, DNA polymerase, and MCM10-ID using three glide-based molecular docking algorithms: HTVS, SP and XP to produce a robust calculation. All four proteins are crucial proteins that actively participate in CC development, and inhibiting them together can be a game-changer step for multitargeted drug designing. Our multitargeted screening identified Sodium (Na) Danshensu, a natural FDA-approved phenolic compound of caffeic acid derivatives isolated from Salvia miltiorrhiza. The docking score ranges from -5.892 to -13.103 Kcal/mol, and the screening study was evaluated with the pharmacokinetics and interaction fingerprinting to identify the pattern of interactions that revealed that the compound has bound to the best site it can be fitted to where maximum bonds were created to make the complex stable. The molecular dynamics simulations for 100 ns were then extended to validate the stability of the protein-ligand complexes. The results provide insight into the repurposing, and Na-danshensu exhibited strong binding affinity and stable complex formation with the target proteins, indicating its potential as a multitargeted drug against CC.Communicated by Ramaswamy H. Sarma.

Unveiling the multitargeted potential of deprodone and control comparison with linezolid against hydrolase and transferase enzymes of methicillin-resistant Staphylococcus aureus

Staphylococcus aureus (S. aureus), commonly found on the skin and nose, causes minor skin conditions to life-threatening diseases, including boils or impetigo, pneumonia, and bloodstream infections. MRSA (Methicillin-Resistant S. aureus) is a strain resistant to many antibiotics and poses a significant challenge in clinical settings. Nowadays, the alternative drug Linezolid is used, and it is not clear when MRSA starts resistance to it, necessitating the need for more alternative drugs with the least chance of developing resistance. This study aims to identify a multitargeted drug candidate with better efficacy than Linezolid. We have taken three hydrolase and transferase proteins from S. aureus, performed the multitargeted docking studies with human-approved drugs, and compared them with the control drug Linezolid. The docking and MM\GBSA scores ranging from -6.79 to -5.78 Kcal/mol and - 37.47 to 30.16 Kcal/mol, respectively, that revealed Deprodone (used for inflammatory skin disorders, bowel disease, and fatty acid metabolism disorders) can be a far better and multitargeted drug candidate than Linezolid. We extended our studies to include extensive pharmacokinetics and molecular interaction fingerprints for interaction pattern studies. Also, the DFT computations optimised the drug, and we extended our studies for MD Simulation in water for 100 ns, which showed the complexes among the identified drug with proteins are entirely stable with acceptable deviation, fluctuations and many intermolecular interactions that make them stable. We also performed the MM\GBSA studies on MD simulation's all 1000 frames to understand the complex energy level. All the results reveal promising interactions between Deprodone and the targeted enzymes, suggesting its potential as a multitargeted therapeutic agent-however, experimental studies need to validate Deprodone against MRSA.

Reporting multitargeted potency of Tiaprofenic acid against lung cancer: Molecular fingerprinting, MD simulation, and MTT-based cell viability assay studies

Lung Cancer (LC) is among the most death-causing cancers, has caused the most destruction and is a gender-neutral cancer, and WHO has kept this cancer on its priority list to find the cure. We have used high-throughput virtual screening, standard precision docking, and extra precise docking for extensive screening of Drug Bank compounds, and the uniqueness of this study is that it considers multiple protein targets of prognosis and metastasis of LC. The docking and MM\GBSA calculation scores for the Tiaprofenic acid (DB01600) against all ten proteins range from -8.422 to -5.727 kcal/mol and - 47.43 to -25.72 kcal/mol, respectively. Also, molecular fingerprinting helped us to understand the interaction pattern of Tiaprofenic acid among all the proteins. Further, we extended our analysis to the molecular dynamic simulation in a neutralised SPC water medium for 100 ns. We analysed the root mean square deviation, fluctuations, and simulative interactions among the protein, ligand, water molecules, and protein-ligand complexes. Most complexes have shown a deviation of <2 Å as cumulative understanding. Also, the fluctuations were lesser, and only a few residues showed the fluctuation with a huge web of interaction between the protein and ligand, providing an edge that supports that the protein and ligand complexes were stable. In the MTT-based Cell Viability Assay, Tiaprofenic Acid exhibited concentration-dependent anti-cancer efficacy against A549 lung cancer cells, significantly reducing viability at 100 μg/mL. These findings highlight its potential as a therapeutic candidate, urging further exploration into the underlying molecular mechanisms for lung cancer treatment.

Monte Carlo simulations for free energies of hydration: Past to present

A summary of the development of Monte Carlo statistical mechanics simulations for the computation of free energies of hydration of organic molecules is followed by presentation of results with the latest version of the optimized potentials for liquid simulations-all atom force field and the TIP4P water model. Scaling of the Lennard-Jones interactions between water, oxygen, and carbon atoms by a factor of 1.25 is found to improve the accuracy of free energies of hydration for 50 prototypical organic molecules from a mean unsigned error of 1.0-1.2 to 0.4 kcal/mol.

Unveiling the potency of FDA-approved oxidopamine HBr for cervical cancer regulation and replication proteins

Cervical Cancer remains a women's health concern worldwide and ranks among the most prevalent cancers, particularly in developing countries. Many women are diagnosed with cervical cancer, with a substantial number succumbing to the disease even after the availability of vaccines and drugs. The tumour microenvironment often exhibits immune evasion, including suppression of T-cell activity and altered cytokine, impacting the efficacy of therapeutic interventions and highlighting the need for treatments to modulate the immune response. Despite efforts to promote HPV vaccination and regular screenings, it causes many deaths, underscoring the urgent need for continued research, healthcare access, and rapid drug development or repurposing. In this study, we identified various proteins involved in cervical cancer cell cycle regulation and DNA replication proteins, performed the multitargeted docking with an FDA-approved library, and identified Oxidopamine HBr as a multitargeted drug. Studies extended with pharmacokinetics and compared with the standard values followed by DFT, which supported the compound as a multitargeted inhibitor. Further, the docked complexes were taken for the interaction fingerprints, and it was identified that there are many 9 polar, 5 hydrophobic, 2 aromatic, and 2 basic residues. We extended our studies for 100ns MD Simulation in water, and the computations explored the deviation and fluctuations under 2Å and many intermolecular interactions; the same trajectory files were used for the MM\GBSA studies. All the studies have supported the Oxidopamine HBr as a cervical cancer multitargeted inhibitor-however, experimental studies are needed before human use.

Equilibration of linear polyethylene melts with pre-defined molecular weight distributions employing united atom Monte Carlo simulations

Possessing control over the molecular size (molecular weight/chain length/degree of polymerization) distribution of a polymeric material is extremely important in applications. This is manifested de facto by the extensive contemporary scientific literature on processes for controlling this distribution experimentally. Yet, the literature on computational techniques for achieving prescribed molecular size distributions in simulations and exploring their impact on properties is much less abundant than its experimental/technical counterpart. Here, we develop-on the basis of united atom melt simulations employing connectivity-altering Monte Carlo moves-a new Metropolis selection criterion that drives the multichain system to a prescribed but otherwise arbitrary distribution of molecular sizes. The new formulation is a generalization of that originally proposed [P. V. K. Pant and D. N. Theodorou, Macromolecules 28, 7224 (1995)], but simpler and more computationally efficient. It requires knowledge solely of the target distribution, which need not be normalized. We have implemented the new formulation on long-chain linear polyethylene melts, obtaining excellent results. The target molecular size distribution can be provided in tabulated form, allowing absolute freedom as to the types of chain size profiles that can be simulated. Distributions for which equilibration has been achieved here for linear polyethylene include a truncated most probable, a truncated Schulz-Zimm, an arbitrary one defined in tabulated form, a broad truncated Gaussian, and a bimodal Gaussian. The last two are comparable to those encountered in industrial applications. The impact of the molecular size distribution on the properties of the simulated melts, such as density, chain dimensions, and mixing thermodynamics, is explored.

Integrative analysis discovers Imidurea as dual multitargeted inhibitor of CD69, CD40, SHP2, lysozyme, GATA3, cCBL, and S-cysteinase from SARS-CoV-2 and M. tuberculosis

Two of the deadliest infectious diseases, COVID-19 and tuberculosis (TB), have combined to establish a worldwide pandemic, wreaking havoc on economies and claiming countless lives. The optimised, multitargeted medications may diminish resistance and counter them together. Based on computational expression studies, 183 genes were co-expressed in COVID-19 and TB blood samples. We used the multisampling screening algorithms on the top ten co-expressed genes (CD40, SHP2, Lysozyme, GATA3, cCBL, SIVmac239 Nef, CD69, S-adenosylhomocysteinase, Chemokine Receptor-7, and Membrane Protein). Imidurea is a multitargeted inhibitor for COVID-19 and TB, as confirmed by extensive screening and post-filtering utilising MM\GBSA algorithms. Imidurea has shown docking and MM\GBSA scores of -8.21 to -4.75 Kcal/mol and -64.16 to -29.38 Kcal/mol, respectively. The DFT, pharmacokinetics, and interaction patterns suggest that Imidurea may be a drug candidate, and all ten complexes were tested for stability and bond strength using 100 ns for all MD atoms. The modelling findings showed the complex's repurposing potential, with a cumulative deviation and fluctuation of <2 Å and significant intermolecular interaction, which validated the possibilities. Finally, an inhibition test was performed to confirm our in-silico findings on SARS-CoV-2 Delta variant infection, which was suppressed by adding imidurea to Vero E6 cells after infection.

Identification of 5-nitroindazole as a multitargeted inhibitor for CDK and transferase kinase in lung cancer: a multisampling algorithm-based structural study

Lung cancer is the second most common cancer, which is the leading cause of cancer death worldwide. The FDA has approved almost 100 drugs against lung cancer, but it is still not curable as most drugs target a single protein and block a single pathway. In this study, we screened the Drug Bank library against three major proteins- ribosomal protein S6 kinase alpha-6 (6G77), cyclic-dependent protein kinase 2 (1AQ1), and insulin-like growth factor 1 (1K3A) of lung cancer and identified the compound 5-nitroindazole (DB04534) as a multitargeted inhibitor that potentially can treat lung cancer. For the screening, we deployed multisampling algorithms such as HTVS, SP and XP, followed by the MM\GBSA calculation, and the study was extended to molecular fingerprinting analysis, pharmacokinetics prediction, and Molecular Dynamics simulation to understand the complex's stability. The docking scores against the proteins 6G77, 1AQ1, and 1K3A were - 6.884 kcal/mol, - 7.515 kcal/mol, and - 6.754 kcal/mol, respectively. Also, the compound has shown all the values satisfying the ADMET criteria, and the fingerprint analysis has shown wide similarities and the water WaterMap analysis that helped justify the compound's suitability. The molecular dynamics of each complex have shown a cumulative deviation of less than 2 Å, which is considered best for the biomolecules, especially for the protein-ligand complexes. The best feature of the identified drug candidate is that it targets multiple proteins that control cell division and growth hormone mediates simultaneously, reducing the burden of the pharmaceutical industry by reducing the resistance chance.

Molecular interaction and MD-simulations: investigation of Sizofiran as a promising anti-cancer agent targeting eIF4E in colorectal cancer

CRC has a major global health impact due to high mortality rates. CRC shows high expression of eukaryotic translation initiation factor (eIF4E) protein, the rapid development of lung, bladder, colon, prostate, breast, head, and neck cancer is attributed to the dysregulation of eIF4E making an important target for treatment. Targeting eIF4E-mediated translation is a promising anti-cancer strategy. Many organic compounds that inhibit eIF4E are being studied clinically. The compound Sizofiran has emerged as a promising eIF4E inhibitor candidate, but its exact mechanism of action is unclear. In an effort to close this discrepancy by clarifying the mechanism of the interactions between phytochemical substances and eIF4E, molecular docking and dynamics studies were conducted. Molecular docking studies found Sizofiran (- 12.513 kcal/mol) has the most affinity eIF4E binding energy out of 93 phytochemicals, 5 current drugs, and 4 known inhibitors. This positions it as a top eIF4E inhibitor candidate. An alignment of eIF4E protein sequences from multiple pathogens revealed that the glutamate103 interacting residues are evolutionarily conserved across the different eIF4E proteins. Further insights from 100 ns of MD simulations supported Sizofiran having superior stability and eIF4E inhibition compared to reference compounds. Designed Sizofiran-related compounds showed better activity than the current drugs such as Camptosar, Sorafenib, Regorafenib, Doxorubicin, and Kenpaullone, indicating strong potential to suppress CRC progression by targeting eIF4E. This research aims to significantly aid development of improved eIF4E-targeting drugs for cancer treatment.

Graphical abstract

Showing the Graphical abstract of the complete study.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-024-00206-3.

Chlordiazepoxide against signalling, receptor and regulatory proteins of breast cancer: a structure-based in-silico approach

Among the most prevalent forms of cancer are breast, lung, colon-rectum, and prostate cancers, and breast cancer is a major global health challenge, contributing to 2.26 million cases with approximately 685,000 deaths worldwide in 2020 alone, typically beginning in the milk ducts or lobules that produce and transport milk during lactation and it is becoming challenging to treat as the tissues are developing resistance, which makes urgent calls for new multitargeted drugs. The multitargeted drug design provides a better solution, simultaneously targeting multiple pathways, even when the drug resists one, it remains effective for others. In this study, we included four crucial proteins that perform signalling, receptor, and regulatory action, namely- NUDIX Hydrolases, Dihydrofolate Reductase, HER2/neu Kinase and EGFR and performed multitargeted molecular docking studies against human-approved drugs using HTVS, SP and extra precise algorithms and filtered the poses with MM\GBSA, suggested a benzodiazepine derivative chlordiazepoxide, used as an anxiolytic agent, can be a multitargeted inhibitor with docking and MM\GBSA score ranging from - 4.628 to - 7.877 and - 18.59 to - 135.86 kcal/mol, respectively, and the most interacted residues were 6ARG, 6GLU, 3TRP, and 3VAL. The QikProp-based ADMET and DFT computations showed the suitability and stability of the drug candidate followed by 100 ns MD simulation in water and MMGBSA on trajectories, resulting in stable performance and many intermolecular interactions to make the complexes stable, which favours that chlordiazepoxide can be a multitargeted breast cancer inhibitor. However, experimental validation is needed before its use.

Mitoxantrone 2HCl's adroit activity against cervical cancer replication and maintenance proteins: a multitargeted approach

Cervical cancer poses a significant global health challenge, ranking as the fourth most common cancer among women worldwide and resulting in approximately 300,000 deaths yearly, predominantly caused by high-risk human papillomavirus strains (HPV), mainly types 16 and 18. The scenario poses the urgent need of the hour to develop effective treatment strategies that can address the complexity of cervical cancer and multitargeted inhibitor designing that holds promise as it can simultaneously target multiple proteins and pathways involved in its progression and have the potential to enhance treatment efficacy, reduce the likelihood of drug resistance. In this study, we have performed multitargeted molecular docking of FDA-approved drugs against cervical cancer replication and maintenance proteins- Xenopus kinesin-like protein-2 (3KND), cell division cycle protein-20 (4N14), MCM2-histone complex (4UUZ) and MCM6 Minichromosome maintenance (2KLQ) with HTVS, SP and XP algorithms and have obtained the docking and MM\GBSA score ranging from -8.492 to -5.189 Kcal/mol and -58.16 to -39.07 Kcal/mol. Further, the molecular interaction fingerprints identified ALA, THR, SER, ASN, LEU, and ILE were among the most interacted residues, leaning towards hydrophobic and polar amino acids. The pharmacokinetics and DFT of the compound have shown promising results. The complexes were simulated for 100 ns to study the stability by computing the deviation, fluctuations, and intermolecular interactions formed during the simulation. This study produced promising results, satisfying the criteria that Mitoxantrone 2HCl can be a multitargeted inhibitor against cervical cancer proteins-however, experimental validation is a must before human use.Communicated by Ramaswamy H. Sarma.

Multisampling-based docking reveals Imidazolidinyl urea as a multitargeted inhibitor for lung cancer: an optimisation followed multi-simulation and in-vitro study

Lung Cancer is one of the deadliest cancers, responsible for more than 1.80 million deaths annually worldwide, and it is on the priority list of WHO. In the current scenario, when cancer cells become resistant to the drug, making it less effective leaves the patient in vulnerable conditions. To overcome this situation, researchers are constantly working on new drugs and medications that can help fight drug resistance and improve patients' outcomes. In this study, we have taken five main proteins of lung cancer, namely RSK4 N-terminal kinase, guanylate kinase, cyclin-dependent kinase 2, kinase CK2 holoenzyme, tumour necrosis factor-alpha and screened the prepared Drug Bank library with 1,55,888 compounds against all using three Glide-based docking algorithms namely HTVS, standard precision and extra precise with a docking score ranging from -5.422 to -8.432 Kcal/mol. The poses were filtered with the MM\GBSA calculations, which helped to identify Imidazolidinyl urea C11H16N8O8 (DB14075) as a multitargeted inhibitor for lung cancer, validated with advanced computations like ADMET, interaction pattern fingerprints, and optimised the compound with Jaguar, producing satisfied relative energy. All five complexes were performed with MD Simulation for 100 ns with NPT ensemble class, producing cumulative deviation and fluctuations < 2 Å and a web of intermolecular interaction, making the complexes stable. Further, the in-vitro analysis for morphological imaging, Annexin V/PI FACS assay, ROS and MMP analysis caspase3//7 activity were performed on the A549 cell line producing promising results and can be an option to treat lung cancer at a significantly cheaper state.Communicated by Ramaswamy H. Sarma.

Structure-Based In Silico Approaches Reveal IRESSA as a Multitargeted Breast Cancer Regulatory, Signalling, and Receptor Protein Inhibitor

Breast cancer begins in the breast cells, mainly impacting women. It starts in the cells that line the milk ducts or lobules responsible for producing milk and can spread to nearby tissues and other body parts. In 2020, around 2.3 million women across the globe received a diagnosis, with an estimated 685,000 deaths. Additionally, 7.8 million women were living with breast cancer, making it the fifth leading cause of cancer-related deaths among women. The mutational changes, overexpression of drug efflux pumps, activation of alternative signalling pathways, tumour microenvironment, and cancer stem cells are causing higher levels of drug resistance, and one of the major solutions is to identify multitargeted drugs. In our research, we conducted a comprehensive screening using HTVS, SP, and XP, followed by an MM/GBSA computation of human-approved drugs targeting HER2/neu, BRCA1, PIK3CA, and ESR1. Our analysis pinpointed IRESSA (Gefitinib-DB00317) as a multitargeted inhibitor for these proteins, revealing docking scores ranging from -4.527 to -8.809 Kcal/mol and MM/GBSA scores between -49.09 and -61.74 Kcal/mol. We selected interacting residues as fingerprints, pinpointing 8LEU, 6VAL, 6LYS, 6ASN, 5ILE, and 5GLU as the most prevalent in interactions. Subsequently, we analysed the ADMET properties and compared them with the standard values of QikProp. We extended our study for DFT computations with Jaguar and plotted the electrostatic potential, HOMO and LUMO regions, and electron density, followed by a molecular dynamics simulation for 100 ns in water, showing an utterly stable performance, making it a suitable drug candidate. IRESSA is FDA-approved for lung cancer, which shares some pathways with breast cancers, clearing the hurdles of multitargeted drugs against breast and lung cancer. This has the potential to be groundbreaking; however, more studies are needed to concreate IRESSA's role.

Molecular screening reveals Variolin B as a multitargeted inhibitor of lung cancer: a molecular docking-based fingerprinting and molecular dynamics simulation study

Lung Cancer is the topmost death causing cancer and results from smoking, air pollution, cigar, exposure to asbestos or radon-like substances, and genetic factors. The cases of Lung Cancer in south Asian developing nations are being seen most due to heavy pollution and unbalanced lifestyle and putting a considerable burden on healthcare systems. The Food and Drug Administration of the USA has approved almost 100 drugs against SCLC and NSLC and a few drugs that are given to minimise the side effect of anticancer drugs. However, the drugs are shown to be resistant at significantly higher stages and non-affective on cancerous cells and have long-term side effects due to designing the drug by keeping one protein/gene target while designing or repurposing the drugs. In this study, we have taken five main lung cancer protein targets- Nerve growth factor protein (1SG1), Apoptosis inhibitor survivin (1XOX), Heat shock protein (3IUC), Protein tyrosine phosphate (3ZM3), Aldo-keto reductase (4XZL) and screened the complete prepared Drug Bank library of 155888 compounds and identified Variolin B (DB08694) as a multitargeted inhibitor against lung cancer using HTVS, SP and XP sampling algorithms followed by MM\GBSA calculation to sort the best pose. Variolin B is a natural marine antitumor and antiviral compound, so we analysed the ADMET properties and interaction patterns and then simulated all five P-L complexes for 100 ns in water using the NPT ensemble to check its selves against lung cancer. The docking results, ADMET and fingerprints have shown a good performance, and RMSD and RMSF results were with least deviation and fluctuations (<2Å) and produced a huge contact with other residues making the complex stable. The complexes initially fluctuated and deviated due to changes in the solute medium and sudden heat and stabilise after a few ns. However, extensive experimental validation is required before human use.Communicated by Ramaswamy H. Sarma.

Multitargeted inhibitory effect of Mitoxantrone 2HCl on cervical cancer cell cycle regulatory proteins: a multitargeted docking-based MM\GBSA and MD simulation study

Cervical cancer remains a significant global health concern that starts in the cervix, the lower part of the uterus that connects to the vagina and is caused by the human papillomavirus (HPV), necessitating the development of effective multitargeted effective and resistance-proof therapies. In early-stage cervical cancer may not show any symptoms, however, as the cancer progresses, some people may experience- abnormal vaginal bleeding, watery or bloody vaginal discharge, pain in the pelvis or lower back, pain during sex, and frequent and painful urination. In this study, we screened the complete FDA-approved drug library using a multitargeted inhibitory approach against four cervical cancer proteins, namely mitotic arrest deficient -2, DNA polymerase epsilon B-subunit, benzimidazole-related -1, and threonine-protein kinase-1 which crucially plays its role for the in its development process. We employed the HTVS, SP and XP algorithms for efficient filtering and screening that helped to identify Mitoxantrone 2HCl against all of them with docking and MM\GBSA scores ranging from - 11.63 to - 7.802 kcal/mol and - 74.38 to - 47.73 kcal/mol, respectively. We also evaluated the interaction patterns of each complex and the pharmacokinetics properties that helped gain insight into interactions. Subsequently, we performed multiscale MD simulations for 100 ns to understand the dynamic behaviour and stability of the Mitoxantrone 2HCl -protein complexes that revealed the formation of stable drug-protein complexes and provided insights into the molecular interactions that contribute to Mitoxantrone's inhibitory effects on these proteins and can be a better drug for cervical cancer. However, experimental studies of these findings could pave the way for therapies to combat cervical cancer effectively.

Unveiling the multitargeted repurposing potential of taxifolin (dihydroquercetin) in cervical cancer: an extensive MM\GBSA-based screening, and MD simulation study

Cervical cancer is a significant cause of morbidity and mortality in women worldwide. Despite the availability of effective therapies, the development of drug resistance and adverse side effects remain significant challenges in cervical cancer treatment. Thus, repurposing existing drugs as multitargeted therapies for cervical cancer is an attractive approach. In this study, we extensively screened the complete prepared FDA-approved drugs and identified the repurposing potential of taxifolin, a flavonoid with known antioxidant and anti-inflammatory properties, as a multitargeted therapy for cervical cancer. We performed a computational analysis using molecular docking with various sampling algorithms, namely HTVS, SP, and XP algorithms, for robust sampling pose and filtered with MM/GBSA analysis to determine the binding affinity of taxifolin with potential targets involved in cervical cancer, such as Symmetric Mad2 Dimer, replication initiation factor MCM10-ID, TPX2, DNA polymerase epsilon B-subunit, human TBK1, and alpha-v beta-8. We then conducted MD simulations to investigate the stability and conformational changes of the complex formed between taxifolin and the mentioned proteins. Our results suggest that taxifolin has a high binding affinity ranging from - 6.094 to - 9.558 kcal/mol, indicating its potential as a multitargeted therapy for cervical cancer. Furthermore, interaction fingerprints, pharmacokinetics and MD simulations revealed that the Taxifolin-target complexes remained stable over the simulation period, indicating that taxifolin may bind to the targets for an extended period. Our study suggests that taxifolin has the potential as a multitargeted therapy for cervical cancer, and further experimental studies are necessary to validate our findings.

SHP-1 tyrosine phosphatase binding to c-Src kinase phosphor-dependent conformations: A comparative structural framework

SHP-1 is a cytosolic tyrosine phosphatase that is primarily expressed in hematopoietic cells. It acts as a negative regulator of numerous signaling pathways and controls multiple cellular functions involved in cancer pathogenesis. This study describes the binding preferences of SHP-1 (pY536) to c-Srcopen (pY416) and c-Srcclose (pY527) through in silico approaches. Molecular dynamics simulation analysis revealed more conformational changes in c-Srcclose upon binding to SHP-1, as compared to its active/open conformation that is stabilized by the cooperative binding of the C-SH2 domain and C-terminal tail of SHP-1 to c-Src SH2 and KD. In contrast, c-Srcclose and SHP-1 interaction is mediated by PTP domain-specific WPD-loop (WPDXGXP) and Q-loop (QTXXQYXF) binding to c-Srcclose C-terminal tail residues. The dynamic correlation analysis demonstrated a positive correlation for SHP-1 PTP with KD, SH3, and the C-terminal tail of c-Srcclose. In the case of the c-Srcopen-SHP-1 complex, SH3 and SH2 domains of c-Srcopen were correlated to C-SH2 and the C-terminal tail of SHP-1. Our findings reveal that SHP1-dependent c-Src activation through dephosphorylation relies on the conformational shift in the inhibitory C-terminal tail that may ease the recruitment of the N-SH2 domain to phosphotyrosine residue, resulting in the relieving of the PTP domain. Collectively, this study delineates the intermolecular interaction paradigm and underlying conformational readjustments in SHP-1 due to binding with the c-Src active and inactive state. This study will largely help in devising novel therapeutic strategies for targeting cancer development.

An in-silico investigation of fluoride ions impact on pancreatic lipase

Fluorine is a halogen beneficial to teeth and bones at a lower concentration. But in excess, it is a toxin and causes adverse effects. Fluoride is toxic to enzymes generally when it inhibits the enzyme activity involved in metabolic pathways. Here we study invitro and invivo findings on the interaction of fluoride on the enzymes Aconitase, Adenylyl cyclase, Arginase, Cytochrome-c-oxidase, Glucose-6-phosphatase, Protein phosphatase, Succinate dehydrogenase from liver and lipase from pancreas by using molecular docking and simulations to gain insights into the mechanism by which fluoride modifies the activity of pancreatic lipase. our molecular modeling and docking studies identified that lipase is the most strongly inhibited enzyme compared to other enzymes mentioned above with -0.42 Kcal/mol binding energy and 495.78 milli molar of predicted IC50 value with interaction with Phe227 residue. To further validate this, we have taken the lipase enzyme in presence of fluoride ions for molecular dynamic simulations of 100 ns. To analyze the impact of fluoride ions on the lipase dynamics, two different simulations of 100 ns each were performed. In one simulation, we have simulated lipase in its apo form in the aqueous environment without any fluoride ions and in another simulation lipase in its apo form was kept in the presence of randomly placed fluoride ions countered with sodium ions to maintain the pH as neutral. The simulation analysis revealed that major fluctuations in lipase was observed between 230 and 300 residues in presence of fluoride ions. Interestingly, this is the exact location of the "lid" like acting loop of residues responsible for the inward/outward movement of the substrate to lipase catalytically active site containing catalytic triad of residues Leu153, His263, and Pro177. His263 residue random flip is believed to be the critical incident that causes the substrate's inward/outward movement at the catalytically active site coordinated by "lid" opening, providing enough space for the substrate.

Molecular docking analysis of mefluhybenamine with lung cancer targets

Lung cancer is the most prevalent type of cancer worldwide, with 2.21 million cases and 1.80 million fatalities in 2020. The main factor influencing lung cancer is smoking, and the most common form of lung cancer, non-small cell lung cancer (NSCLC), accounts for around 80% of instances compared to small cell carcinoma, and about 75% of patients are already in an advanced stage when they are detected. Despite significant early detection and therapy improvements, the five-year survival rate for NSCLC is not encouraging. Therefore, it is essential to look into the molecular origins of non-small cell lung cancer to develop more effective therapeutic strategies-the binding affinities and energy landscape with the proteins. Cyclin Dependent kinase 2 (CDK2) and Insulin-like Growth Factor 1 Receptor (IGF1) were more substantial and sustained in lung cancer that was chosen as the two primary target proteins in this. We screened the entire Drug Bank-prepared library of 1,55,888 compounds and found (2R,3R)-7-(Methylsulfonyl)-3-(2,4,5-trifluorophenyl) -1,2,3,4-tetrahydropyrido[1,2-a] benzimidazol-2-aminium (Mefluhybenamine) to be a significant inhibitor. Mefluhybenamine showed strong hydrogen bonding and other bonding topologies, such as van der Waals force, in its high docking scores of -6.168 Kcal/mol and -5.26 Kcal/mol, and ADMET results showed excellent bioavailability, remarkable solubility, no side effects, and toxicity. The molecular dynamicsimulation confirmed the compound's stability and interaction pattern for 100 ns in an SPC water medium with the slightest deviation and fluctuation. Data shows that Mefluhybenamine is a potential candidate. However, validation of the compound is essential.

Hairy Gels: A Computational Study

We present results of MD and MC simulations of the equilibrium properties of swelling gels with comb-like or bottlebrush subchains and compare them to scaling-theory predictions. In accordance with theory, the simulation results demonstrate that swelling coefficient of the gel increases as a function of the polymerization degree of the main chains and exhibits a very weak maximum (or is virtually constant) as a function of the polymerization degree and grafting density of side chains. The bulk osmotic modulus passes through a shallow minimum as the polymerization degree of the side chains increases. This minimum is attributed to the onset of overlap of side chains belonging to different bottlebrush strands in the swollen gel.

Macrophage-Targeted Punicalagin Nanoengineering to Alleviate Methotrexate-Induced Neutropenia: A Molecular Docking, DFT, and MD Simulation Analysis

Punicalagin is the most bioactive pomegranate polyphenol with high antioxidant and free-radical scavenging activity and can potentially cure different ailments related to the cardiovascular system. The current research work was envisioned to predict the targeting efficiency of punicalagin (PG) nanoparticles to the macrophages, more specifically to bone marrow macrophages. For this, we selected mannose-decorated PLGA-punicalagin nanoparticles (Mn-PLGA-PG), and before formulating this nanocarrier in laboratory settings, we predicted the targeting efficiency of this nanocarrier by in silico analysis. The analysis proceeded with macrophage mannose receptors to be acquainted with the binding affinity and punicalagin-based nanocarrier interactions with this receptor. In silico docking studies of macrophage mannose receptors and punicalagin showed binding interactions on its surface. PG interacted with hydrogen bonds to the charged residue ASP668 and GLY666 and polar residue GLN760 of the Mn receptor. Mannose with a docking score of −5.811 Kcal/mol interacted with four hydrogen bonds and the mannose receptor of macrophage, and in PLGA, it showed a −4.334 Kcal/mol docking score. Further, the analysis proceeded with density functional theory analysis (DFT) and HOMO–LUMO analysis, followed by an extensive 100 ns molecular dynamics simulation to analyse the trajectories showing the slightest deviation and fluctuation. While analysing the ligand and protein interaction, a wonderful interaction was found among the atoms of the ligand and protein residues. This computational study confirms that this nanocarrier could be a promising lead molecule to regulate the incidence of drug-induced neutropenia. Furthermore, experimental validation is required before this can be stated with complete confidence or before human use.

Conceptual density functional theory under pressure: Part I. XP-PCM method applied to atoms

High pressure chemistry offers the chemical community a range of possibilities to control chemical reactivity, develop new materials and fine-tune chemical properties. Despite the large changes that extreme pressure brings to the table, the field has mainly been restricted to the effects of volume changes and thermodynamics with less attention devoted to electronic effects at the molecular scale. This paper combines the conceptual DFT framework for analyzing chemical reactivity with the XP-PCM method for simulating pressures in the GPa range. Starting from the new derivatives of the energy with respect to external pressure, an electronic atomic volume and an atomic compressibility are found, comparable to their enthalpy analogues, respectively. The corresponding radii correlate well with major known sets of this quantity. The ionization potential and electron affinity are both found to decrease with pressure using two different methods. For the electronegativity and chemical hardness, a decreasing and increasing trend is obtained, respectively, and an electronic volume-based argument is proposed to rationalize the observed periodic trends. The cube of the softness is found to correlate well with the polarizability, both decreasing under pressure, while the interpretation of the electrophilicity becomes ambiguous at extreme pressures. Regarding the electron density, the radial distribution function shows a clear concentration of the electron density towards the inner region of the atom and periodic trends can be found in the density using the Carbó quantum similarity index and the Kullback-Leibler information deficiency. Overall, the extension of the CDFT framework with pressure yields clear periodic patterns.

E2UbcH5B-derived peptide ligands target HECT E3-E2 binding site and block the Ub-dependent SARS-CoV-2 egression: A computational study

Homologous to E6AP carboxyl-terminus (HECT)-type E3 ligase performs ubiquitin (Ub)-proteasomal protein degradation via forming a complex with E2∼Ub. Enveloped viruses including SARS-CoV-2 escape from the infected cells by harnessing the E-class vacuolar protein-sorting (ESCRT) machinery and mimic the cellular system through PPAY motif-based linking to HECT Ub ligase activity. In the present study, we have characterized the binding pattern of E2^UbcH5B to HECT domains of NEDD4L, WWP1, WWP2, HECW1, and HECW2 through in silico analysis to isolate the E2^UbcH5B-specific peptide inhibitors that may target SARS-CoV-2 viral egression. Molecular dynamics analysis revealed more opening of E2^UbcH5B-binding pocket upon binding to HECT^NEDD4L, HECT^WWP1, HECT^WWP2, HECT^HECW1, and HECT^HECW2. We observed similar binding pattern for E2^UbcH5B and mentioned HECT domains as previously reported for HECT^NEDD4L where Trp762, Trp709, and Trp657 residues of HECT^NEDD4L, HECT^WWP1, and HECT^WWP2 are involved in making contacts with Ser94 residue of E2^UbcH5B. Similarly, corresponding to HECT^NEDD4L Tyr756 residue, HECT^WWP1, HECT^WWP2, HECT^HECW1, and HECT^HECW2-specific Phe703, Phe651, Phe1387, and Phe1353 residues execute interaction with E2^UbcH5B. Our analysis suggests that corresponding to Cys942 of HECT^NEDD4L, Cys890, Cys838, Cys1574, and Cys1540 residues of HECT^WWP1, HECT^WWP2, HECT^HECW1, and HECT^HECW2, respectively are involved in E2-to-E3 Ub transfer. Furthermore, MM-PBSA free energy calculations revealed favorable energy values for E2^UbcH5B-HECT complexes along with the individual residue contributions. Subsequently, two E2^UbcH5B-derived peptides (His55-Phe69 and Asn81-Ala96) were tested for their binding abilities against HECT domains of NEDD4L, WWP1, WWP2, HECW1, and HECW2. Their binding was validated through substitution of Phe62, Pro65, Ile84, and Cys85 residues into Ala, which revealed an impaired binding, suggesting that the proposed peptide ligands may selectively target E2-HECT binding and Ub-transfer. Collectively, we propose that peptide-driven blocking of E2-to-HECT Ub loading may limit SARS-CoV-2 egression and spread in the host cells.

A comparative in silico study to detect the effect of food-additives on metabolic protein and its perturbations compensated by osmolytes

Since its inception, food additive has been an integral part of the food processing industry with various commercial roles. Besides its advantages, various studies have already highlighted its long-term adverse effects on human health. However, in terms of protein structures and functions, the innate mechanism that triggers these effects has not been elucidated in previously reported studies. Our work takes an in silico approach to delve into structural implications resulting from these additives with three well studied metabolic proteins-lysozyme, bovine serum albumin (BSA) and ribonuclease A. Three classes of food additives- synthetic color, preservatives, and phosphate-containing, are taken here to understand their effects on the aforementioned metabolic proteins. Conventional molecular docking and dynamics (MD) studies reveal that these additives induce significant structural perturbations. Among them, carmoisine brings about the most secondary structural changes for lysozyme and ribonuclease A, whereas sodium tripolyphosphate affects BSA the most. To restore the secondary structural loss, we further examine the roles of osmolytes through cross-docking and higher timescale MD simulations. These studies unravel that application of osmolytes like raffinose and trehalose triggers structural restoration for BSA, lysozyme and ribonuclease A, and highlight their roles as co-formulants to alleviate the adverse effects of food additives.

Inter-subunit crosstalk via PDZ synergistically governs allosteric activation of proapoptotic HtrA2

The mitochondrial serine protease High-temperature requirement A2 (HtrA2) is associated with various diseases including neurodegenerative disorders and cancer. Despite availability of structural details, the reports on HtrA2's mechanistic regulation that varies with the type of activation signals still remain non-concordant. To expound the role of regulatory PDZ (Postsynaptic density-95/Discs large/Zonula occludens-1) domains in multimodal activation of HtrA2, we generated heterotrimeric HtrA2 variants comprising different numbers of PDZs and/or active-site mutations. Sequential deletion of PDZs from the trimeric ensemble significantly affected its residual activity in a way that proffered a hypothesis advocating inter-molecular allosteric crosstalk via PDZs in HtrA2. Furthermore, structural and computational snapshots affirmed the role of PDZs in secondary structural element formation around the regulatory loops and coordinated reorganization of the N-terminal region. Therefore, apart from providing cues for devising structure-guided therapeutic strategies, this study establishes a physiologically relevant working model of complex allosteric regulation through a trans-mediated cooperatively shared energy landscape.

Design of a Multi-Epitopes Based Chimeric Vaccine against Enterobacter cloacae Using Pan-Genome and Reverse Vaccinology Approaches

Enterobacter cloacae (EC) is a significant emerging pathogen that is occasionally associated with lung infection, surgical site infection, urinary infection, sepsis, and outbreaks in neonatal intensive care units. In light of the fact that there is currently no approved vaccine or therapeutic option for the treatment of EC, the current study was developed to concentrate on applications based on modern computational approaches to design a multi-epitope-based E. cloacae peptide vaccine (MEBEPV) expressing the antigenic determinants prioritized from the EC genome. Integrated computational analyses identified two potential protein targets (phosphoporin protein-PhoE and putative outer-membrane porin protein) for further exploration on the basis of pangenome subtractive proteomics and immunoinformatic in-depth examination of the core proteomes. Then, a multi-epitope peptide vaccine was designed, which comprised shortlisted epitopes that were capable of eliciting both innate and adaptive immunity, as well as the cholera toxin’s B-subunit, which was used as an adjuvant in the vaccine formulation. To ensure maximum expression, the vaccine’s 3D structure was developed and the loop was refined, improving the stability by disulfide engineering, and the physicochemical characteristics of the recombinant vaccine sequence were found to be ideal for both in vitro and in vivo experimentation. Blind docking was then used for the prediction of the MEBEPV predominant blinding mode with MHCI, MHCII, and TLR3 innate immune receptors, with lowest global energy of −18.64 kJ/mol, −48.25 kJ/mol, and −5.20 kJ/mol for MHC-I, MHC-II, and TLR-4, respectively, with docked complexes considered for simulation. In MD and MMGBSA investigations, the docked models of MEBEPV-TLR3, MEBEPV-MHCI, and MEBEPV-MHCII were found to be stable during the course of the simulation. MM-GBSA analysis calculated −122.17 total net binding free energies for the TLR3-vaccine complex, −125.4 for the MHC I-vaccine complex, and −187.94 for the MHC II-vaccine complex. Next, MM-PBSA analysis calculated −115.63 binding free energy for the TLR3-vaccine complex, −118.19 for the MHC I-vaccine complex, and −184.61 for the MHC II-vaccine complex. When the vaccine was tested in silico, researchers discovered that it was capable of inducing both types of immune responses (cell mediated and humoral) at the same time. Even though the suggested MEBEPV has the potential to be a powerful contender against E. cloacae-associated illnesses, further testing in the laboratory will be required before it can be declared safe and immunogenic.

The Role of Grain Boundaries in the Corrosion Process of Fe Surface: Insights from ReaxFF Molecular Dynamic Simulations

Intergranular corrosion is the most common corrosion phenomenon in Fe-based alloys. To better understand the mechanism of intergranular corrosion, the influence of grain boundaries on Fe-H2O interfacial corrosion was studied using molecular dynamics simulation based on a new Fe-H2O reaction force field potential. It is found that the corrosion rate at the polycrystalline grain boundary is significantly faster than that of twin crystals and single crystals. By the analysis of stress, it can be found that the stress at the polycrystalline grain boundary and the sigma5 twin grain boundary decreases sharply during the corrosion process. We believe that the extreme stress released at the grain boundary will promote the dissolution of Fe atoms. The formation of vacancies on the Fe matrix surface will accelerate the diffusion of oxygen atoms. This leads to the occurrence of intergranular corrosion.

Purification, Characterization and Functional Site Prediction of the Vaccinia-related Kinase 2A Small Transmembrane Domain

Vaccinia-related kinases (VRK) are serine-threonine kinases that regulate several signaling pathways. The isoform-VRK2A of one such kinase VRK2 controls cell stress response by interacting with TAK1, a mitogen-activated protein 3 kinase (MAP3K), via its partly cytosolic C-terminal transmembrane domain (VTMD). To establish the driving force and identify the key residues of the VRK2A-TAK1 interaction, we expressed and purified the standalone 3.6 kDa VTMD in the bacterial system using a unique and atypical two-step approach, when the effort to obtain full-length VRK2A remained unsuccessful. Characterization of biophysical properties demonstrated that VTMD domain maintains its structural integrity. Furthermore, dissecting the VRK2A-TAK1 binding interface using in silico tools provided important cues toward engineering the VRK2A-TAK1 interface to modulate its functions with desired characteristics. Most importantly, this novel purification strategy demonstrates its universal applicability in protein biochemistry research by serving as a model system for obtaining difficult-to-purify small proteins or domains.•

VRK2A is a highly disordered transmembrane (TM) kinase, whose TM domain interacts with TAK1 (transforming growth factor-β-activated kinase).

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The standalone VRK2A-TM domain (VTMD) was purified using affinity chromatography followed by two-step centricon based approach.

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Biophysical and in silico analyses confirmed structural integrity of the domain.

Reexamining equations of state of oblate hard ellipsoids of revolution: Numerical simulation utilizing a cluster Monte Carlo algorithm and comparison to virial theory

We provide highly accurate equation-of-state data determined by means of cluster Monte Carlo simulations for the isotropic phase of oblate hard ellipsoids of revolution. Both equation-of-state data and phase boundaries of the isotropic phase are obtained from relatively large ensembles with typically 1000 particles. The comparison of simulation data with a virial approach gives evidence for the importance of high-order so-far-unknown virial coefficients and therewith many-particle interactions in dense, isotropic systems of anisotropic particles. While a virial approach with a rescaled Carnahan-Starling correction for the unknown, higher-order virial coefficients reproduces the simulation data of moderately anisotropic particles with high accuracy, we suggest for highly anisotropic shapes a simple, heuristic equation of state as a suitable approach.

Molecular dynamics and structural analysis of the binding of COP1 E3 ubiquitin ligase to β-catenin and TRIB pseudokinases

Tribbles pseudokinases, Tribbles homolog 1 (TRIB1), Tribbles homolog 2 (TRIB2), and Tribbles homolog 3 (TRIB3), bind to constitutive photomorphogenesis protein 1 (COP1) E3 ligase to mediate the regulation of β-catenin expression. The interaction mechanism between COP1 E3 ligase and β-catenin has not been addressed to date. Based on the functional presence of TRIBs in wingless-related integration site (WNT) signaling, we analyzed their interaction patterns with β-catenin and COP1. Here, through in silico approaches, we ascribe the COP1 binding pattern against TRIBs and β-catenin. TRIB1 (355-DQIVPEY-361), TRIB2 (326-DQLVPDV-332), and TRIB3 (333-AQVVPDG-339) peptides revealed a shallow binding pocket at the COP1 interface to accommodate the V-P sequence motif. Reinvigoration of the comparative binding pattern and subtle structural analysis via docking, molecular dynamics simulations, molecular mechanics Poisson-Boltzmann surface area, topological, and tunnel analysis revealed that both β-catenin phosphodegron (DSGXXS) and TRIB (D/E/AQXVPD/E) motifs occupied a common COP1 binding site. Current study suggests a structural paradigm of TRIB homologs bearing a conserved motif that may compete with β-catenin phosphodegron signature for binding to WD40 domain of COP1. Thorough understanding of the structural basis for TRIB-mediated regulation of WNT/β-catenin signaling may help in devising more promising therapeutic strategy for liver and colorectal cancers.

Pan-vaccinomics approach towards a universal vaccine candidate against WHO priority pathogens to address growing global antibiotic resistance

Antimicrobial resistance (AMR) in bacterial pathogens is a major global distress. Due to the slow progress of antibiotics development and the fast pace of resistance acquisition, there is an urgent need for effective vaccines against such bacterial pathogens. In-silico approaches including pan-genomics, subtractive proteomics, reverse vaccinology, immunoinformatics, molecular docking, and dynamics simulation studies were applied in the current study to identify a universal potential vaccine candidate against the 18 multi-drug resistance (MDRs) bacterial pathogenic species from a WHO priority list. Ten non-redundant, non-homologous, virulent, and antigenic vaccine candidates were filtered against all targeted species. Nine B-cell-derived T-cell antigen epitopes which show a great affinity to the dominant HLA allele (DRB1*0101) in the human population were screened from selected vaccine candidates using immunoinformatics approaches. Screened epitopes were then used to design a multi-epitope peptide vaccine construct (MEPVC) along with β-defensin adjuvant to improve the immunogenic properties of the proposed vaccine construct. Molecular docking and MD simulation were carried out to study the binding affinity and molecular interaction of MEPVC with human immune receptors (TLR2, TLR3, TLR4, and TLR6). The final MEPVC construct was reverse translated and in-silico cloned in the pET28a(+) vector to ensure its effectiveness. This in silico construct is expected to be helpful for vaccinologists to assess its immune protection effectiveness in vivo and in vitro to counter rising antibiotic resistance worldwide.

Monte Carlo simulations in the unconstrained ensemble

The unconstrained ensemble describes completely open systems whose control parameters are the chemical potential, pressure, and temperature. For macroscopic systems with short-range interactions, thermodynamics prevents the simultaneous use of these intensive variables as control parameters, because they are not independent and cannot account for the system size. When the range of the interactions is comparable with the size of the system, however, these variables are not truly intensive and may become independent, so equilibrium states defined by the values of these parameters may exist. Here, we derive a Monte Carlo algorithm for the unconstrained ensemble and show that simulations can be performed using the chemical potential, pressure, and temperature as control parameters. We illustrate the algorithm by applying it to physical systems where either the system has long-range interactions or is confined by external conditions. The method opens up an avenue for the simulation of completely open systems exchanging heat, work, and matter with the environment.

Elucidating the role of GRIM-19 as a substrate and allosteric activator of pro-apoptotic serine protease HtrA2

HtrA2 (high-temperature requirement A2) and GRIM-19 (gene associated with retinoic and interferon-induced mortality 19 protein) are involved in various biological functions with their deregulation leading to multiple diseases. Although it is known that the interaction between GRIM-19 with HtrA2 promotes the pro-apoptotic activity of the latter, the mechanistic details remained elusive till date. Moreover, designing allosteric modulators of HtrA2 remains obscure due to lack of adequate information on the mode of interaction with its natural substrates cum binding partners. Therefore, in this study, we have unfolded the interaction between HtrA2 and GRIM-19 so as to understand its subsequent functional repercussions. Using in silico analyses and biochemical assays, we identified the region in GRIM-19 that is involved in protein-protein interaction with HtrA2. Furthermore, we have presented a comprehensive illustration of HtrA2's cleavage site specificity. Quantitative analysis using enzyme kinetics underscored the role of GRIM-19 in significant allosteric activation of HtrA2. Overall, this is an extensive study that not only defines HtrA2-GRIM-19 interaction, but also creates a framework for developing strategies toward allosteric regulation of HtrA2 for future therapeutic interventions.

Systematic formulation of thermodynamic properties in the NpT ensemble

Molecular expressions for thermodynamic properties and derivatives of the Gibbs energy up to third order in the isobaric-isothermal (NpT) ensemble are systematically derived using the methodology developed by Lustig for the microcanonical and canonical ensembles [J. Chem. Phys. 100, 3048 (1994)10.1063/1.466446; Mol. Phys. 110, 3041 (2012)10.1080/00268976.2012.695032]. They are expressed by phase-space functions, which represent derivatives of the Gibbs energy with respect to temperature and pressure. Additionally, expressions for the phase-space functions for temperature-dependent potentials are provided, which, for example, are required when quantum corrections, e.g., Feynman-Hibbs corrections, are applied in classical simulations. The derived expressions are validated by Monte Carlo simulations for the simple Lennard-Jones model fluid at three selected state points. A unique result is that the phase-space functions contain only ensemble averages of combinations of powers of enthalpy and volume. Thus, the calculation of thermodynamic properties in the NpT ensemble does not require volume derivatives of the potential energy. This is particularly advantageous in Monte Carlo simulations when the interactions between molecules are described by empirical force fields or very accurate ab initio pair and nonadditive three-body potentials.

Loss of GSK-3β mediated phosphorylation in HtrA2 contributes to uncontrolled cell death with Parkinsonian phenotype

HtrA2, a proapoptotic mitochondrial serine protease, promotes cellular protection against oxidative damage. Literature reports show positive correlation between loss of HtrA2 protease activity and Parkinson's Disease (PD) susceptibility. Homozygous loss-of-function mutations in murine-HtrA2, and when they rarely occur in humans result in severe neurodegeneration and infantile death. Here, we report a novel heterozygous pathogenic HTRA2 variant, c.725C > T (p.T242M) in Indian PD patients. Although, this mutation exhibits no significant conformational changes compared to the wild-type, functional studies with HtrA2-T242M transfected neurons reveal common features of PD pathogenesis such as dysfunction, altered morphology and mitochondrial membrane depolarization. Despite exhibiting two-fold decrease in enzyme activity, observation of excessive cell-death due to over-expression of the mutant has been correlated with it being constitutively active. This interesting behavioral anomaly has been attributed to the loss of phosphorylation-mediated regulatory checkpoint at the T242M mutation site that is otherwise controlled by glycogen synthase kinase-3β (GSK-3β). This study, with seamless amalgamation of biophysical and biomedical research unravels a mechanistic pathway of HtrA2 regulation and delineates its biological role in PD. Therefore, this investigation will not only prove beneficial toward devising therapeutic strategies against HtrA2-associated diseases mediated by GSK-3β but also suggest new avenues for treatment of Parkinsonian phenotype.

Dual specificity phosphatase 9: A novel binding partner cum substrate of proapoptotic serine protease HtrA2

Human high temperature requirement protease A2 (HtrA2) is a trimeric PDZ bearing proapoptotic serine protease, which is involved in various cellular processes and pathologies. Research in the last decade strongly advocates its role as a potential therapeutic target and therefore warrants the need to minutely investigate its mechanism of action, regulation, interactions with other proteins and its binding specificities. In this particular study, we adopted an in silico approach to predict novel interacting partners and/or substrates of HtrA2 by building a peptide library using a binding pattern search. This library was used to look for novel ligand proteins in the human proteome. Thereafter, the putative interaction was validated using biochemical and cell-based studies. In a first, here we report that HtrA2 shows robust interactions with DUSP9 (Dual specificity phosphatase 9) in GST-pulldown and Co-Immunoprecipitation (Co-IP) experiments and cleaves it in vitro. Besides, we also provided a detailed characterization of the interaction interface. Moreover, this study in general provides an efficient, fast and practical method of candidate ligand library screening for exploring the binding properties of HtrA2.

The central role of entropy in adiabatic ensembles and its application to phase transitions in the grand-isobaric adiabatic ensemble

Entropy has become increasingly central to characterize, understand, and even guide assembly, self-organization, and phase transition processes. In this work, we build on the analogous role of partition functions (or free energies) in isothermal ensembles and that of entropy in adiabatic ensembles. In particular, we show that the grand-isobaric adiabatic (μ, P, R) ensemble, or Ray ensemble, provides a direct route to determine the entropy. This allows us to follow the variations of entropy with the thermodynamic conditions and thus explore phase transitions. We test this approach by carrying out Monte Carlo simulations on argon and copper in bulk phases and at phase boundaries. We assess the reliability and accuracy of the method through comparisons with the results from flat-histogram simulations in isothermal ensembles and with the experimental data. Advantages of the approach are multifold and include the direct determination of the μ-P relation, without any evaluation of pressure via the virial expression, the precise control of the system size (number of atoms) via the input value of R, and the straightforward computation of enthalpy differences for isentropic processes, which are key quantities to determine the efficiency of thermodynamic cycles. A new insight brought by these simulations is the highly symmetric pattern exhibited by both systems along the transition, as shown by scaled temperature-entropy and pressure-entropy plots.

A distinct concerted mechanism of structural dynamism defines activity of human serine protease HtrA3

Human HtrA3 (high-temperature requirement protease A3) is a trimeric multitasking propapoptotic serine protease associated with critical cellular functions and pathogenicity. Implicated in diseases including cancer and pre-eclampsia, its role as a tumor suppressor and potential therapeutic target cannot be ignored. Therefore, elucidating its mode of activation and regulatory switch becomes indispensable towards modulating its functions with desired effects for disease intervention. Using computational, biochemical and biophysical tools, we delineated the role of all domains, their combinations and the critical phenylalanine residues in regulating HtrA3 activity, oligomerization and specificity. Our findings underline the crucial roles of the N-terminus as well as the PDZ domain in oligomerization and formation of a catalytically competent enzyme, thus providing new insights into its structure–function coordination. Our study also reports an intricate ligand-induced allosteric switch, which redefines the existing hypothesis of HtrA3 activation besides opening up avenues for modulating protease activity favorably through suitable effector molecules.

Evidence for NAD+-dependent histone dynamics and tunneling associated conformational transitions in circadian deacetylase SIRT1

Circadian rhythm is a biological cycle that is involved in all processes over 24 h day and night period. Sirtuin 1 (SIRT1) is a 747 amino acid-long class III Nicotinamide adenine dinucleotide (NAD⁺)-dependent histone that acts as a circadian deacetylase. Here we present a detailed in-silico analysis to address comparative structure-function relationship and interaction pattern of SIRT1-NAD⁺/Zn⁺² and SIRT1^NAD+/Zn+2-acetylated histone H4 (H4^KAC16) complexes. MD-based ensemble analysis suggested an overall loss of helical content (21.144-17.230%) in H4^KAC16-bound SIRT1^NAD+/Zn+2 due to conformational readjustments of 32 residues, as compared to SIRT1^NAD+/Zn+2. Due to increased flexibility, SIRT1-specific SER275, SER442 and ARG466 residues involved in NAD⁺ association facilitated in the formation of a transient tunnel (17.77 Å) that was further elongated to 19.25 Å upon SIRT1^NAD+/Zn+2 binding to H4^KAC16. A close conformation of SIRT1^NAD+/Zn+2 was achieved due to binding of H4^KAC16 that results in the movement of helical module towards Zn⁺² binding module together with Rossmann fold at NAD⁺ binding region. Furthermore, a 2-fold increase (4.31-8.82 Å) in the measured inter-atomic distance between imidazole nitrogen of conserved HIS363 and NAD⁺-specific 2'-hydroxyl group of ribose ring was evident in SIRT1^NAD+/Zn+2-H4^KAC16 complex. At 90 ns time scale, the distance between C6A of adenine ring and C2N of nicotinamide ring was more extended (19.32 Å) in SIRT1^NAD+/Zn+2-H4^KAC16 as compared to SIRT1^NAD+/Zn+2 (11.54 Å). These data suggest that H4^KAC16 binding to SIRT1 may coordinate an unusual conformational readjustment of nicotinamide ring at site-b and reposition of HIS363 to facilitate SIRT1-dependent deacetylase activity. Taken together, our findings will help in understanding the precise structural changes occurring in response to SIRT1 deacetylase activity of core histone.

Wood–Moisture Relationships Studied with Molecular Simulations: Methodological Guidelines

This paper aims at providing a methodological framework for investigating wood polymers using atomistic modeling, namely, molecular dynamics (MD) and grand canonical Monte Carlo (GCMC) simulations. Atomistic simulations are used to mimic water adsorption and desorption in amorphous polymers, make observations on swelling, mechanical softening, and on hysteresis. This hygromechanical behavior, as observed in particular from the breaking and reforming of hydrogen bonds, is related to the behavior of more complex polymeric composites. Wood is a hierarchical material, where the origin of wood-moisture relationships lies at the nanoporous material scale. As water molecules are adsorbed into the hydrophilic matrix in the cell walls, the induced fluid–solid interaction forces result in swelling of these cell walls. The interaction of the composite polymeric material, that is the layer S2 of the wood cell wall, with water is known to rearrange its internal material structure, which makes it moisture sensitive, influencing its physical properties. In-depth studies of the coupled effects of water sorption on hygric and mechanical properties of different polymeric components can be performed with atomistic modeling. The paper covers the main components of knowledge and good practice for such simulations.

Identification of a distal allosteric ligand binding pocket in HtrA3

Human HtrA3 (High temperature requirement protease A3) is a trimeric PDZ bearing propapoptotic serine protease, which is involved in various diseases including cancer and pre-eclampsia. Proposed to be a tumor suppressor, its role as a potential therapeutic target is strongly advocated. Therefore, it becomes imperative to gain insights into its mechanism of action and regulation. Allostery is a well-known mechanism of catalytic activation for many HtrA3 homologs, which opens up avenues for manipulating enzyme functions for therapeutic intervention. In our study, through in silico and biochemical approaches, we have reported for the first time that HtrA3 shows allosteric behaviour. We identified a novel selective binding pocket, which triggers conformational reorientations through signal propagation to the distantly situated active-site pocket via the functionally important loop regions. Using molecular docking, simulation studies and biochemical studies we have identified the regulatory movements at and around the active site pocket. Our study is the first one to report a non-classical binding site for HtrA3, which is instrumental for formation of a catalytically efficient orthosteric pocket upon substrate binding.

Discerning the mechanism of action of HtrA4: a serine protease implicated in the cell death pathway

High-temperature requirement protease A4 (HtrA4) is a secretary serine protease whose expression is up-regulated in pre-eclampsia (PE) and hence is a possible biomarker of PE. It has also been altered in cancers such as glioblastoma, breast carcinoma, and prostate cancer making it an emerging therapeutic target. Among the human HtrAs, HtrA4 is the least characterized protease pertaining to both structure and its functions. Although the members of human HtrA family share a significant structural and functional conservation, subtle structural changes have been associated with certain distinct functional requirements. Therefore, intricate dissection of HtrA4 structural and functional properties becomes imperative to understand its role in various biological and pathophysiological processes. Here, using inter-disciplinary approaches including in silico, biochemical and biophysical studies, we have done a domain-wise dissection of HtrA4 to delineate the roles of the domains in regulating oligomerization, stability, protease activity, and specificity. Our findings distinctly demonstrate the importance of the N-terminal region in oligomerization, stability and hence the formation of a functional enzyme. In silico structural comparison of HtrA4 with other human HtrAs, enzymology studies and cleavage assays with X-linked inhibitor of apoptosis protein (XIAP) show overall structural conservation and allosteric mode of protease activation, which suggest functional redundancy within this protease family. However, significantly lower protease activity as compared with HtrA2 indicates an additional mode of regulation of the protease activity in the cellular milieu. Overall, these studies provide first-hand information on HtrA4 and its interaction with antiapoptotic XIAP thus implicating its involvement in the apoptotic pathway.

Molecular simulations by generalized-ensemble algorithms in isothermal-isobaric ensemble

Generalized-ensemble algorithms are powerful techniques for investigating biomolecules such as protein, DNA, lipid membrane, and glycan. The generalized-ensemble algorithms were originally developed in the canonical ensemble. On the other hand, not only temperature but also pressure is controlled in experiments. Additionally, pressure is used as perturbation to study relationship between function and structure of biomolecules. For this reason, it is important to perform efficient conformation sampling based on the isothermal-isobaric ensemble. In this article, we review a series of the generalized-ensemble algorithms in the isothermal-isobaric ensemble: multibaric-multithermal, pressure- and temperature-simulated tempering, replica-exchange, and replica-permutation methods. These methods achieve more efficient simulation than the conventional isothermal-isobaric simulation. Furthermore, the isothermal-isobaric generalized-ensemble simulation samples conformations of biomolecules from wider range of temperature and pressure. Thus, we can estimate physical quantities more accurately at any temperature and pressure values. The applications to the biomolecular system are also presented.

Structural basis of βTrCP1-associated GLI3 processing

Controlled ubiquitin-mediated protein degradation is essential for various cellular processes. GLI family regulates the transcriptional events of the sonic hedgehog pathway genes that are implicated in almost one fourth of human tumors. GLI3 phosphorylation by Ser/Thr kinases is a primary factor for their transcriptional activity that incurs the formation of both GLI3 repressor and activator forms. GLI3 processing is triggered in an ubiquitin-dependent manner via SCF^βTrCP1 complex; however, structural characterization, mode of action based on sequence of phosphorylation signatures and induced conformational readjustments remain elusive. Here, through structural analysis and molecular dynamics simulation assays, we explored comparative binding pattern of GLI3 phosphopeptides against βTrCP1. A comprehensive and thorough analysis demarcated GLI3 presence in the binding cleft shared by inter-bladed binding grooves of β-propeller. Our results revealed the involvement of all seven WD40 repeats of βTrCP1 in GLI3 interaction. Conversely, GLI3 phosphorylation pattern at primary protein kinase A (PKA) sites and secondary casein kinase 1 (CK1) or glycogen synthase kinase 3 (GSK3) sites was carefully evaluated. Our results indicated that GLI3 processing depends on the 19 phosphorylation sites (849, 852, 855, 856, 860, 861, 864, 865, 868, 872, 873, 876, 877, 880, 899, 903, 906, 907 and 910 positions) by a cascade of PKA, GSK3β and CSKI kinases. The presence of a sequential phosphorylation in the binding induction of GLI3 and βTrCP1 may be a hallmark to authenticate GLI3 processing. We speculate that mechanistic information of the individual residual contributions through structure-guided approaches may be pivotal for the rational design of specific and more potent inhibitors against activated GLI3 with a special emphasis on the anticancer activity.