Improved side-chain torsion potentials for the Amber ff99SB protein force field

Click estradiol dimers with novel aromatic bridging units: synthesis and anticancer evaluation

Estradiol dimers (EDs) possess significant anticancer activity by targeting tubulin dynamics. In this study, we synthesised 12 EDs variants via copper-catalysed azide-alkyne cycloaddition (CuAAC) reaction, focusing on structural modifications within the aromatic bridge connecting two estradiol moieties. In vitro testing of these EDs revealed a marked improvement in selectivity towards cancerous cells, particularly for ED1-8. The most active compounds, ED3 (IC50 = 0.38 μM in CCRF-CEM) and ED5 (IC50 = 0.71 μM in CCRF-CEM) demonstrated cytotoxic effects superior to 2-methoxyestradiol (IC50 = 1.61 μM in CCRF-CEM) and exhibited anti-angiogenic properties in an endothelial cell tube-formation model. Cell-based experiments and in vitro assays revealed that EDs interfere with mitotic spindle assembly. Additionally, we proposed an in silico model illustrating the probable binding modes of ED3 and ED5, suggesting that dimers with a simple linker and a single substituent on the aromatic central ring possess enhanced characteristics compared to more complex dimers.

Evaluation of inhibition effect and interaction mechanism of antiviral drugs on main protease of novel coronavirus: Molecular docking and molecular dynamics studies

The outbreak of pneumonia caused by the novel coronavirus (SARS-CoV-2) has presented a challenge to public health. The identification and development of effective antiviral drugs is essential. The main protease (3CLpro) plays an important role in the viral replication of SARS-CoV-2 and is considered to be an effective therapeutic target. In this study, according to the principle of drug repurposing, a variety of antiviral drugs commonly used were studied by molecular docking and molecular dynamics (MD) simulations to obtain potential inhibitors of main proteases. 24 antiviral drugs were docked with 5 potential action sites of 3CLpro, and the drugs with high binding strength were further simulated by MD and the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) binding free energy calculations. The results showed that the drugs with high flexibility could bind to 3CLpro better than those with low flexibility. The interaction mechanism between antiviral drugs and main protease was analyzed in detail by calculating the root mean square displacement (RMSD), root mean square fluctuation (RMSF) and interaction residues properties. The results showed that the six drugs with high flexibility (Remdesivir, Simnotrelvir, Sofosbuvir, Ledipasvir, Indinavir and Raltegravir) had strong binding strength with 3CLpro, and the last four antiviral drugs can be used as potential candidates for main protease inhibitors.

Dy-SheHeRASADe: A representation of the β sheet dynamics through surface descriptors

Molecular dynamics (MD) simulations are important tools for studying the dynamic motions of macromolecules at the atomic level. With the increasing capabilities of high performance computing, MD simulations are becoming more widely used. This allows molecular modelers to simulate the molecular behavior of large molecular architectures for much longer trajectories. Appropriate visualization of MD trajectories is becoming essential to provide an immediate and intuitive understanding of a molecule's dynamics and function. In this study, we implement a novel 3D graphical representation, Dynamical Sheets Helper for RepresentAtion of SurfAce Descriptors (Dy-SheHeRASADe), to visualize the β sheet secondary structures of proteins in the context of molecular dynamics. Dy-SheHeRASADe is developed in UnityMol, an open source molecular viewer and prototyping platform. We considered β sheet fluctuations and hydrogen bond formation during molecular dynamics simulations to characterize the parts of β sheets with large motions or with labile bonds. We propose two visualization modes based on a surface representation of the β sheets calculated according to the positions of the α carbons and the hydrogen bonds between the β strands. The volumetric mode, in which this surface is enclosed in a semi-transparent volume that represents the fluctuation zone of the sheet during dynamics. The heatmap mode, in which the surface is colored according to the amplitude values of the α carbons. In addition, we quantify the β sheet fluctuations by displaying the values of the largest and smallest movements of the β sheets, the surface area of the sheets, and the number of hydrogen bonds.

An in-silico approach to target multiple proteins involved in anti-microbial resistance using natural compounds produced by wild mushrooms

Bacterial resistance to antibiotics and the number of patients infected by multi-drug-resistant bacteria have increased significantly over the past decade. This study follows a computational approach to identify potential antibacterial compounds from wild mushrooms. Twenty-six known compounds produced by wild mushrooms were docked to assess their affinity with drug targets of antibiotics such as penicillin-binding protein-1a (PBP1a), DNA gyrase, and isoleucyl-tRNA synthetase (ILERS). Docking scores were further validated by multiple receptor conformer (MRC)-based docking studies. Based on the MRC-based docking results, eight molecules were shortlisted for ADMET analysis. Molecular dynamics (MD) simulations were further performed to evaluate the conformational stability of the ligand-protein complexes. Binding energies were computed by the gmx_MMPBSA method. The data were obtained in terms of root-mean square deviation, and root-mean square fluctuation justified the stability of Austrocortilutein A, Austrocortirubin, and Confluentin in complex with several proteins under physiological conditions. Among these, Austrocortilutein A displayed better binding affinity with PBP1a and ILERS when compared with their respective reference ligands. This study is preliminary and aims to help drive the search for compounds that have the capacity to overcome the anti-microbial resistance of prevalent bacteria, using natural compounds produced by wild mushrooms. Further experimental validation is required to justify the clinical use of the studied compounds.

Modification of MM force fields around heme-Fe in the CYP-ligand complex and ab initio FMO calculations for the complex

Cytochrome P450 (CYP) enzymes play essential roles in the synthesis and metabolic activation of physiologically active substances. CYP has a prosthetic heme (iron protoporphyrin IX) in its active center, where Fe ion (heme-Fe) is deeply involved in enzymatic reactions of CYP. To precisely describe the structure and electronic states around heme-Fe, we modified the force fields (FFs) around heme-Fe in molecular mechanics (MM) simulations and conducted ab initio fragment molecular orbital (FMO) calculations for the CYP-ligand complex. To describe the coordination bond between heme-Fe and its coordinated ligand (ketoconazole), we added FF between heme-Fe and the N atom of ketoconazole, and then the structure of the complex was optimized using the modified FF. Its adequacy was confirmed by comparing the MM-optimized structure with the X-ray crystal one of the CYP-ketoconazole complex. We also performed 100 ns molecular dynamics simulations and revealed that the coordination bonds around heme-Fe were maintained even at 310 K and that the CYP-ketoconazole structure was kept similar to the X-ray structure. Furthermore, we investigated the electronic states of the complex using the ab initio FMO method to identify the CYP residues and parts of ketoconazole that contribute to strong binding between CYP and ketoconazole. The present procedure of constructing FF between heme-Fe and ketoconazole can be applicable to other CYP-ligand complexes, and the modified FF can provide their accurate structures useful for predicting the specific interactions between CYP and its ligands.

Unveiling a Hidden Pocket in HIV-1 Protease: New Insights Into Retroviral Protease Cantilever-Tip Region Characteristics

The HIV-1 protease is critical for the process of viral maturation and as such, it is one of the most well characterized proteins in the Protein Data Bank. There is some evidence to suggest that the HIV-1 protease is capable of accommodating small molecule fragments at several locations on its surface outside of the active site. However, some pockets on the surface of proteins remain unformed in the apo structure and are termed "cryptic sites." To date, no cryptic sites have been identified in the structure of HIV-1 protease. Here, we characterize a novel cryptic cantilever pocket on the surface of the HIV-1 protease through mixed-solvent molecular dynamics simulations using several probes. Interestingly, we noted that several homologous retroviral proteases exhibit evolutionarily conserved dynamics in the cantilever region and possess a conserved pocket in the cantilever region. Immobilization of the cantilever region of the HIV-1 protease via disulfide cross-linking resulted in curling-in of the flap tips and the propensity for the protease to adopt a semi-open flap conformation. Structure-based analysis and fragment-based screening of the cryptic cantilever pocket suggested that the pocket may be capable of accommodating ligand structures. Furthermore, molecular dynamics simulations of a top scoring fragment bound to the cryptic pocket illustrated altered flap dynamics of the fragment-bound enzyme. Together, these results suggest that the mobility of the cantilever region plays a key role in the global dynamics of retroviral proteases. Therefore, the cryptic cantilever pocket of the HIV-1 protease may represent an interesting target for future in vitro studies.

Discovering novel Cathepsin L inhibitors from natural products using artificial intelligence

Cathepsin L (CTSL) is a promising therapeutic target for metabolic disorders. Current pharmacological interventions targeting CTSL have demonstrated potential in reducing body weight gain, serum insulin levels, and improving glucose tolerance. However, the clinical application of CTSL inhibitors remains limited. In this study, we used a combination of artificial intelligence and experimental methods to identify new CTSL inhibitors from natural products. Through a robust deep learning model and molecular docking, we screened 150 molecules from natural products for experimental validation. At a concentration of 100 µM, we found that 36 of them exhibited more than 50 % inhibition of CTSL. Notably, 13 molecules displayed over 90 % inhibition and exhibiting concentration-dependent effects. The molecular dynamics simulation on the two most potent inhibitors, Plumbagin and Beta-Lapachone, demonstrated stable interaction at the CTSL active site. Enzyme kinetics studies have shown that these inhibitors exert an uncompetitive inhibitory effect on CTSL. In conclusion, our research identifies Plumbagin and Beta-Lapachone as potential CTSL inhibitors, offering promising candidates for the treatment of metabolic disorders and illustrating the effectiveness of artificial intelligence in drug discovery.

Investigating how HIV-1 antiretrovirals differentially behave as substrates and inhibitors of P-glycoprotein via molecular dynamics simulations

HIV-1 can rapidly infect the brain upon initial infection, establishing latent reservoirs that induce neuronal damage and/or death, resulting in HIV-Associated Neurocognitive Disorder. Though anti-HIV-1 antiretrovirals (ARVs) suppress viral load, the blood-brain barrier limits drug access to the brain, largely because of highly expressed efflux proteins like P-glycoprotein (P-gp). While no FDA-approved P-gp inhibitor currently exists, HIV-1 protease inhibitors show promise as partial P-gp inhibitors, potentially enhancing drug delivery to the brain. Herein, we employed docking and molecular dynamics simulations to elucidate key differences in P-gp's interactions with several antiretrovirals, including protease inhibitors, with known inhibitory or substrate-like behaviors towards P-gp. Our results led us to hypothesize new mechanistic details of small-molecule efflux by and inhibition of P-gp, where the "Lower Pocket" in P-gp's transmembrane domain serves as the primary initial site for small-molecule binding. Subsequently, this pocket merges with the more traditionally studied drug binding site-the "Upper Pocket"-thus funneling small-molecule drugs, such as ARVs, towards the Upper Pocket for efflux. Furthermore, our results reinforce the understanding that both binding energetics and changes in protein dynamics are crucial in discerning small molecules as non-substrates, substrates, or inhibitors of P-gp. Our findings indicate that interactions between P-gp and inhibitory ARVs induce bridging of transmembrane domain helices, impeding P-gp conformational changes and contributing to the inhibitory behavior of these ARVs. Overall, insights gained in this study could serve to guide the design of future P-gp-targeting therapeutics for a wide range of pathological conditions and diseases, including HIV-1.

Synthesis of isoniazid derivatives and evaluation of their α-chymotrypsin inhibitory effect through in silico guided in vitro studies

Alpha-chymotrypsin is a serine protease. Its overexpression is responsible for several ailments, such as chronic obstructive pulmonary disease, autoimmune diseases, pancreatitis, and colon cancers. Therefore, the discovery of potent α-chymotrypsin inhibitors is essential for the treatment of the aforementioned ailments. In this study, we identified new α-chymotrypsin inhibitors through a systematic approach, utilizing the in silico and in vivo studies to predict and confirm the inhibitory potential of isoniazid derivatives. During this study, six compounds 2, 3, 4, 7, 9, and 10 were shortlisted from ten isoniazid derivatives through in silico screening. After that, MD simulations were performed for these compounds. The shortlisted compounds were evaluated through an in vitro α-chymotrypsin inhibitory assay. Compounds 9 and 10 showed a potent inhibition against α-chymotrypsin. The identified compounds or their derivatives can be further investigated as drug leads against the ailments caused by α-chymotrypsin and related serine proteases.

PFOS and PFOSA induce oxidative stress-mediated cardiac defects in zebrafish via PPARγ and AHR pathways, respectively

Perfluorooctane sulfonate (PFOS) and its precursor, perfluorooctane sulfonamide (PFOSA), are widespread in the environment. Evidence suggests a strong link between maternal exposure to PFOS/PFOSA and congenital heart diseases in the offspring, but the underlying mechanisms remain unclear. We hypothesized that PFOS and PFOSA induce cardiac defects through the peroxisome proliferator-activated receptor gamma (PPARγ) and aryl hydrocarbon receptor (AHR) pathways, respectively. In this study, we demonstrated that exposing zebrafish embryos to either PFOSA or PFOS caused cardiac malformations and dysfunction. Both PFOS and PFOSA induced reactive oxygen species (ROS) overproduction, mitochondrial damage, and apoptosis in zebrafish larvae hearts. Blockade of PPARγ through either pharmaceutical inhibition or genetic knockdown only attenuated the changes caused by PFOS, but not those elicited by PFOSA. Conversely, inhibition of AHR alleviated the adverse effects induced by PFOSA but not by PFOS. Both PFOSA and PFOS exhibited similar binding affinities to AHR using molecular docking techniques. The varying ability of PFOS and PFOSA to induce AHR activity in zebrafish embryonic hearts can be attributed to their different capabilities for activating PPARγ. In summary, our findings indicate that PFOS and PFOSA induce excessive ROS production in zebrafish larvae via the PPARγ and AHR pathways, respectively. This oxidative stress in turn causes mitochondrial damage and apoptosis, leading to cardiac defects.

Effects of high pressure processing on structural changes, aggregation, and binding mechanisms of β-Lactoglobulin with typical polyphenols

The binding capacity of β-Lactoglobulin (BLG) is crucial for delivering polyphenols, influenced by structural changes. High pressure processing (HPP) has the potential to modify BLG's structure and aggregation, but its specific impact on BLG-polyphenol interactions is uncertain. This study used circular dichroism spectroscopy and molecular dynamics simulations to reveal HPP-induced structural changes in BLG, supported by particle size analysis indicating aggregation. Seven structurally diverse polyphenols (quercetin-QR, hesperetin-HSP, dihydromyricetin-DHM, gallic acid-GA, (-)-epicatechin-EC, resveratrol-RES, and secoisolariciresinol diglucoside-SDG) were investigated to comprehensively analyze their binding patterns using fluorescence spectroscopy and molecular docking. HPP reduced BLG's ordered structure and increased its aggregation. Binding affinities peaked at 400 MPa for DHM, QR, HSP, GA, and RES, while SDG and EC exhibited maximum affinities at atmospheric pressure and 600 MPa, respectively. Elevated pressures enhanced BLG-polyphenol interactions, particularly at residues 44GLU and 160CYS, with van der Waals forces dominating the binding free energy.

Biocatalytic Ether Lipid Synthesis by an Archaeal Glycerolprenylase

Although ethers are common in secondary natural products, they are an underrepresented functional group in primary metabolism. As such, there are comparably few enzymes capable of constructing ether bonds in a general fashion. However, such enzymes are highly sought after for synthetic applications as they typically operate with higher regioselectivity and under milder conditions than traditional organochemical approaches. To expand the repertoire of well characterized ether synthases, we herein report on a promiscuous archaeal prenyltransferase from the scarcely researched family of geranylgeranylglyceryl phosphate synthases (GGGPSs or G3PSs). We show that the ultrastable Archaeoglobus fulgidus G3PS makes various (E)- and (Z)-configured prenyl glycerol ethers from the corresponding pyrophosphates while exerting perfect control over the configuration at the glycerol unit. Based on experimental and computational data, we propose a mechanism for this enzyme which involves an intermediary prenyl carbocation equivalent. As such, this study provides the fundamental understanding and methods to introduce G3PSs into the biocatalytic alkylation toolbox.

Behind the glow: unveiling the nature of NanoLuc reactants and products

Due to the largely recognized utility of bioluminescence in many fields, a wide variety of luciferase-luciferin systems have been investigated in order to find the best-suited for a number of different applications. The collected knowledge has allowed the identification of a few necessary, or at least desirable, properties, such as bright luminescence, low background signal and small dimension of the enzyme that must exhibit structural stability at operating conditions. The NanoLuc-furimazine pair seems to meet all these requirements, but the mechanism of the reaction and the characteristics of the species responsible for the emission remain unknown. The aim of this study is to identify the luminescent product among the possible forms of oxidized furimazine and to understand how the chemical form and structure of the system, before and after the oxidation, are involved into the reaction mechanism and determine emission. To do this, we consider two possible forms of furimazine, the keto and the enol one, and test which of them is the most plausible candidate in the bioluminescence process on the basis of enzyme-substrate interactions from docking calculations. A similar procedure is repeated for three possible forms of the furimamide luminescent product, and their properties in the protein environment are then evaluated via QM/MM calculations. In contrast with previous indications, our simulations well support the involvement of the enol form of furimazine as reagent and point to the zwitterionic forms of furimamide as emissive species.

Reengineering the Substrate Tunnel to Enhance the Catalytic Efficiency of Squalene Epoxidase

Squalene epoxidase plays a pivotal role in the biosynthesis of ergosterol, its derivatives, and other triterpenoid compounds by catalyzing the transformation of squalene into 2,3-oxidosqualene. However, its low catalytic efficiency remains a primary bottleneck for the microbial synthesis of triterpenoids. In this study, the catalytic activity of the squalene epoxidase from Saccharomyces cerevisiae was significantly improved by reshaping its substrate tunnel, resulting in a marked increase in the yield of the final product, ergosterol. First, the amino acid in the catalytic pocket of squalene epoxidase was replaced with alanine (Ala), effectively reducing the steric hindrance, and thus, enhancing the affinity of the enzyme with its substrate. Then, the V249H/L343A mutant was obtained by redesigning the substrate tunnel of dominant mutant L343A, thus, increasing the titer of ergosterol. The study also elucidated the mechanism behind the increased catalytic activity of the V249H/L343A mutant through substrate tunnel parameter analysis and molecular dynamics simulations. Finally, a titer of 3345 mg/L of ergosterol was achieved by strains containing V249H/L343A in a 5 L bioreactor, with a specific yield of 84 mg/g dry cell weight (DCW), marking a 64% increase compared with the titer achieved by wild type strains. This study established a strong foundation for improving the synthetic efficiency of ergosterol and other triterpenoid compounds.

Coiled Coil Peptide Tiles (CCPTs): Expanding the Peptide Building Block Design with Multivalent Peptide Macrocycles

Owing to their synthetic accessibility and protein-mimetic features, peptides represent an attractive biomolecular building block for the fabrication of artificial biomimetic materials with emergent properties and functions. Here, we expand the peptide building block design space through unveiling the design, synthesis, and characterization of novel, multivalent peptide macrocycles (96mers), termed coiled coil peptide tiles (CCPTs). CCPTs comprise multiple orthogonal coiled coil peptide domains that are separated by flexible linkers. The constraints, imposed by cyclization, confer CCPTs with the ability to direct programmable, multidirectional interactions between coiled coil-forming "edge" domains of CCPTs and their free peptide binding partners. These fully synthetic constructs are assembled using a convergent synthetic strategy via a combination of native chemical ligation and Sortase A-mediated cyclization. Circular dichroism (CD) studies reveal the increased helical stability associated with cyclization and subsequent coiled coil formation along the CCPT edges. Size-exclusion chromatography (SEC), analytical high-performance liquid chromatography (HPLC), and fluorescence quenching assays provide a comprehensive biophysical characterization of various assembled CCPT complexes and confirm the orthogonal colocalization between coiled coil domains within CCPTs and their designed on-target free peptide partners. Lastly, we employ molecular dynamics (MD) simulations, which provide molecular-level insights into experimental results, as a supporting method for understanding the structural dynamics of CCPTs and their complexes. MD analysis of the simulated CCPT architectures reveals the rigidification and expansion of CCPTs upon complexation, i.e., coiled coil formation with their designed binding partners, and provides insights for guiding the designs of future generations of CCPTs. The addition of CCPTs into the repertoire of coiled coil-based building blocks has the potential for expanding the coiled coil assembly landscape by unlocking new topologies having designable intermolecular interfaces.

StreaMD: the toolkit for high-throughput molecular dynamics simulations

Molecular dynamics simulations serve as a prevalent approach for investigating the dynamic behaviour of proteins and protein-ligand complexes. Due to its versatility and speed, GROMACS stands out as a commonly utilized software platform for executing molecular dynamics simulations. However, its effective utilization requires substantial expertise in configuring, executing, and interpreting molecular dynamics trajectories. Existing automation tools are constrained in their capability to conduct simulations for large sets of compounds with minimal user intervention, or in their ability to distribute simulations across multiple servers. To address these challenges, we developed a Python-based tool that streamlines all phases of molecular dynamics simulations, encompassing preparation, execution, and analysis. This tool minimizes the required knowledge for users engaging in molecular dynamics simulations and can efficiently operate across multiple servers within a network or a cluster. Notably, the tool not only automates trajectory simulation but also facilitates the computation of free binding energies for protein-ligand complexes and generates interaction fingerprints across the trajectory. Our study demonstrated the applicability of this tool on several benchmark datasets. Additionally, we provided recommendations for end-users to effectively utilize the tool.Scientific contributionThe developed tool, StreaMD, is applicable to different systems (proteins, ligands and their complexes including co-factors) and requires a little user knowledge to setup and run molecular dynamics simulations. Other features of StreaMD are seamless integration with calculation of MM-GBSA/PBSA binding free energies and protein-ligand interaction fingerprints, and running of simulations within distributed environments. All these will facilitate routine and massive molecular dynamics simulations.

Talin-1 variants associated with spontaneous coronary artery dissection (SCAD) highlight how even subtle changes in multi-functional scaffold proteins can manifest in disease

Variants of talin-1 (TLN1) have recently been linked with spontaneous coronary artery dissection (SCAD) a condition where a tear can form in the wall of a heart artery necessitating immediate medical care. One talin-1 variant, A2013T, has an extensive familial pedigree of SCAD, which led to the screening for, and identification of, further talin-1 variants in SCAD patients. Here we evaluated these variants with commonly used pathogenicity prediction tools and found it challenging to reliably classify SCAD-associated variants, even A2013T where the evidence of a causal role is strong. Using biochemical and cell biological methods, we show that SCAD-associated variants in talin-1, which would typically be classified as non-pathogenic, still cause a measurable impact on protein structure and cell behaviour, including cell movement and wound healing capacity. Together, this indicates that even subtle variants in central mechanosensitive adapter proteins, can give rise to significant health impacts at the individual level, suggesting the need for a possible re-evaluation of the scoring criteria for pathogenicity prediction for talin variants.

Mechanical Unfolding of Network Nodes Drives the Stress Response of Protein-Based Materials

Biomaterials synthesized from cross-linked folded proteins have untapped potential for biocompatible, resilient, and responsive implementations, but face challenges due to costly molecular refinement and limited understanding of their mechanical response. Under a stress vector, these materials combine the gel-like response of cross-linked networks with the mechanical unfolding and extension of proteins from well-defined 3D structures to unstructured polypeptides. Yet the nanoscale dynamics governing their viscoelastic response remains poorly understood. This lack of understanding is further exacerbated by the fact that the mechanical stability of protein domains depends not only on their structure, but also on the direction of the force vector. To this end, here we propose a coarse-grained network model based on the physical characteristics of polyproteins and combine it with the mechanical unfolding response of protein domains, obtained from single molecule measurements and steered molecular dynamics simulations, to explain the macroscopic response of protein-based materials to a stress vector. We find that domains are about 10-fold more stable when force is applied along their end-to-end coordinate than along the other tethering geometries that are possible inside the biomaterial. As such, the macroscopic response of protein-based materials is mainly driven by the unfolding of the node-domains and rearrangement of these nodes inside the material. The predictions from our models are then confirmed experimentally using force-clamp rheometry. This model is a critical step toward developing protein-based materials with predictable response and that can enable applications for shape memory and energy storage and dissipation.

Synthesis, biological evaluation and in silico study of 4-(benzo[d]thiazole-2-yl) phenols based on 4-hydroxy coumarin as acetylcholinesterase inhibitors

Alzheimer's disease, characterized by cognitive decline and memory loss, is associated with decreased acetylcholine levels due to acetylcholinesterase (AChE) activity. Compounds containing a coumarin heterocyclic core coupled with thiazole exhibit excellent acetylcholinesterase inhibitory activity. In this work, we designed and synthesized a series of 4-(benzo[d]thiazole-2-yl) phenols based on 4-hydroxycoumarin. The compounds were synthesized and their inhibitory activities were evaluated through in vitro biological assays. Of the compounds investigated, 3i exhibited the strongest inhibitory activity, with an IC50 value of 2.7 µM. Molecular docking and molecular dynamics simulations were employed to elucidate the binding interactions and stability of the synthesized compounds with AChE. The results demonstrated promising inhibitory activity, suggesting potential therapeutic applications for Alzheimer's disease. This research contributes to the development of coumarin-based heterocyclic compounds as effective AChE inhibitors.

Molecular Modeling of Glycosylated Catalytic Domain of Human Carbonic Anhydrase IX

Glycans exhibit significant structural diversity due to the flexibility of glycosidic bonds linking their constituent monosaccharides and the formation of numerous hydrogen bonds. The present work searches a simulated ensemble of glycan chain conformations attached to the catalytic domain of N-glycosylated human carbonic anhydrase IX (HCA IX-c) to identify conformations pointed away or back-folded toward the protein surface guided by different amino acid residues. A series of classical molecular dynamics (MD) simulation studies for a total of 30 μs followed by accelerated MD simulations for a total of 2 μs have been performed using two different force fields to capture varying degrees of fluctuations of both glycan chain and HCA IX. From the underlying free energy profile and kinetics derived using hidden Markov state model, several stable glycan orientations are identified that extend away from the protein surface and convert among each other with rate constants of the order 107-1010 S-1. Most importantly, we have identified a rare glycan conformation which reaches close to a catalytically important amino acid residue, Glu-106. We further enlist the protein residues that couple such less frequent event of the glycan chain back-folding toward the surface of the protein.

Multispectral and molecular simulation of the interaction of human α1-acid glycoprotein with palbociclib

Palbociclib, a selective CDK4/6 inhibitor with potent anti-tumor effects, was investigated for its interaction with human α1-acid glycoprotein (HAG). Spectral analysis revealed that palbociclib forms a ground state complex with HAG, exhibiting binding constant (Kb) of 104 M-1 at the used temperature range. The interaction between the two was determined to be driven mainly by hydrogen bonding and hydrophobic forces. Multispectral studies indicated that the bound palbociclib altered the secondary structure of HAG and reduced polarity around Trp and Tyr amino acids. And, molecular docking and dynamics simulations verified the experimental findings. Finally, most of the metal ions present in plasma, such as K+, Cu2+, Ca2+, Mg2+, Ni2+, Fe3+, and Co2+, are detrimental to the binding of palbociclib to HAG, with the exception of Zn2+, which is favorable.

Identification of novel broad-spectrum antiviral drugs targeting the N-terminal domain of the FIPV nucleocapsid protein

Coronaviruses pose serious threats to human and animal health worldwide, of which their structural nucleocapsid (N) proteins play multiple key roles in viral replication. However, the structures of animal coronavirus N proteins are poorly understood, posing challenges for research on their functions and pathogenic mechanisms as well as the development of N protein-based antiviral drugs. Therefore, N proteins must be further explored as potential antiviral targets. We determined the structure of the NNTD of feline infectious peritonitis virus (FIPV) and identified 3,6-dihydroxyflavone (3,6- DHF) as an effective N protein inhibitor. 3,6-DHF successfully inhibited FIPV replication in CRFK cells, showing broad-spectrum activity and effectiveness against drugresistant strains. Our study provides important insights for developing novel broadspectrum anti-coronavirus drugs and treating infections caused by drug-resistant mutant strains.

Isovanillin decreases the virulence regulated by the quorum sensing system of Pseudomonas aeruginosa

The quorum-sensing (QS) system of Pseudomonas aeruginosa dominates the pathogenicity of the acute or chronic infection process. Hence, curbing the pathogenicity of P. aeruginosa by targeting QS system is an ideal strategy. This study aims to identify potential anti-virulence compounds that can effectively disrupt the QS system of P. aeruginosa using a combination of virtual screening and experimental validation techniques. We explored inhibitory effect of isovanillin obtained by virtual screening on P. aeruginosa QS regulated virulence factors extracellular protease, biofilm, and pyocyanin. Results displayed that isovanillin could inhibit the virulence phenotypes regulated by the las- and pqs-QS systems of P. aeruginosa. The synthesis of extracellular proteases, pyocyanin, and biofilm formation by P. aeruginosa were dramatically inhibited by sub-MICs doses of isovanillin. The results of RNA sequencing and quantitative PCR revealed that the QS-activated genes down-regulated by subinhibitory isovanillin in the transcriptional evels. Furthermore, the presence of isovanillin increased the susceptibility of drug-resistant P. aeruginosa to kanamycin, meropenem, and polymyxin B. Treatment of isovanillin as a monotherapy significantly decreased the mortality of C. elegans in P. aeruginosa PAO1 or UCBPP-PA14 (PA14) infection. Our study reported the anti-virulence activity of isovanillin against P. aeruginosa, and provided a structural foundation for developing anti-virulence drugs targeting the QS system of P. aeruginosa.

Conformational Dynamics and Molecular Characterization of Alsin MORN Monomer and Dimeric Assemblies

Despite the ubiquity of membrane occupation recognition nexus (MORN) motifs across diverse species in both eukaryotic and prokaryotic organisms, these protein domains remain poorly characterized. Their significance is underscored in the context of the Alsin protein, implicated in the debilitating condition known as infantile-onset ascending hereditary spastic paralysis (IAHSP). Recent investigations have proposed that mutations within the Alsin MORN domain disrupt proper protein assembly, precluding the formation of the requisite tetrameric configuration essential for the protein's inherent biological activity. However, a comprehensive understanding of the relationship between the biological functions of Alsin and its three-dimensional molecular structure is hindered by the lack of available experimental structures. In this study, we employed and compared several protein structure prediction algorithms to identify a three-dimensional structure for the putative MORN of Alsin. Furthermore, inspired by experimental pieces of evidence from previous studies, we employed the developed models to predict and investigate two homo-dimeric assemblies, characterizing their stability. This study's insights into the three-dimensional structure of the Alsin MORN domain and the stability dynamics of its homo-dimeric assemblies suggest an antiparallel linear configuration stabilized by a noncovalent interaction network.

Water-medicated specifically targeting the S1 pockets among serine proteases using an arginine analogue

Because of the high similarity in structure and sequence, it is challenging to distinguish the S1 pocket among serine proteases, primarily due to the only variability at residue 190 (A190 and S190). Peptide or protein-based inhibitors typically target the negatively charged S1 pocket using lysine or arginine as the P1 residue, yet neither discriminates between the two S1 pocket variants. This study introduces two arginine analogues, L-4-guanidinophenylalanine (12) and L-3-(N-amidino-4-piperidyl)alanine (16), as novel P1 residues in peptide inhibitors. 16 notably enhances affinities across all tested proteases, whereas 12 specifically improved affinities towards proteases possessing S190 in the S1 pocket. By crystallography and molecular dynamics simulations, we discovered a novel mechanism involving a water exchange channel at the bottom of the S1 pocket, modulated by the variation of residue 190. Additionally, the specificity of 12 towards the S190-presenting S1 pocket is dependent on this water channel. This study not only introduces novel P1 residues to engineer inhibitory potency and specificity of peptide inhibitors targeting serine proteases, but also unveils a water-mediated molecular mechanism of targeting serine proteases.

Conformational dynamics and ribosomal interactions of Bacillus subtilis Obg in various nucleotide-bound states: Insights from molecular dynamics simulation

Obg, a GTPase, binds to the premature 50S ribosomal subunit and facilitates recruitment of rproteins and rRNA processing to form the mature 50S subunit. This binding depends on nucleotide-induced conformational changes (GDP/GTP). However, the mechanism by which Obg undergoes conformational changes to associate with the premature 50S subunit is unknown. Therefore, 1000 ns molecular dynamics simulations were conducted to investigate this mechanism. Visualization of the simulated trajectory showed that in GDP and GTP-bound states, the C-domain moved towards the SwI region, while in GTP-Mg2+ and ppGpp-bound states, the C-domain shifted towards the N-tails. Further, positioning these conformations of Obg on the 50S subunit suggests possible mechanisms by which the GTP-Mg2+ bound state is responsible for recruiting rprotein, as well as the impact of the absence of Mg2+ in the GTP-bound state. Furthermore, the study provides insights into the conformational changes that may lead to the dissociation of the GDP-bound state from the 50S subunit and explores the potential role of the ppGpp-bound state in inhibiting 70S ribosome formation. Additionally, RMSF and community network analyses reveal how internal dynamics and intricate connections within Obg affect C-domain motion.

Nucleoprotein Phase-Separation Affinities Revealed via Atomistic Simulations of Short Peptide and RNA Fragments

Liquid-liquid phase separation of proteins and nucleic acids into condensate phases is a versatile mechanism for ensuring the compartmentalization of cellular biochemistry. RNA molecules play critical roles in these condensates, particularly in transcriptional regulation and stress responses, exhibiting a wide range of thermodynamic and dynamic behaviors. However, deciphering the molecular grammar that governs the stability and dynamics of protein-RNA condensates remains challenging due to the multicomponent and heterogeneous nature of condensates. In this study, we employ atomistic simulations of 20 distinct mixtures containing minimal RNA and peptide fragments which allows us to dissect the phase-separating affinities of all 20 amino acids in the presence of RNA. Our findings elucidate chemically specific interactions, hydration profiles, and ionic effects that synergistically promote or suppress protein-RNA phase separation. We map a ternary phase diagram of interactions, identifying four distinct groups of residues that promote, maintain, suppress, and disrupt protein-RNA clusters.

A head-to-head comparison of MM/PBSA and MM/GBSA in predicting binding affinities for the CB1 cannabinoid ligands

CONTEXT

The substantial increase in the number of active and inactive-state CB1 receptor experimental structures has provided opportunities for CB1 drug discovery using various structure-based drug design methods, including the popular end-point methods for predicting binding free energies-Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) and Molecular Mechanics/Generalized Born Surface Area (MM/GBSA). In this study, we have therefore evaluated the performance of MM/PBSA and MM/GBSA in calculating binding free energies for CB1 receptor. Additionally, with both MM/PBSA and MM/GBSA being known for their highly individualized performance, we have evaluated the effects of various simulation parameters including the use of energy minimized structures, choice of solute dielectric constant, inclusion of entropy, and the effects of the five GB models. Generally, MM/GBSA provided higher correlations than MM/PBSA (rMM/GBSA = 0.433 - 0.652 vs. rMM/PBSA = 0.100 - 0.486) regardless of the simulation parameters, while also offering faster calculations. Improved correlations were observed with the use of molecular dynamics ensembles compared with energy minimized structures and larger solute dielectric constants. Incorporation of entropic terms led to unfavorable results for both MM/PBSA and MM/GBSA for a majority of the dataset, while the evaluation of the various GB models exerted a varying effect on both the datasets. The findings obtained in this study demonstrate the utility of MM/PBSA and MM/GBSA in predicting binding free energies for the CB1 receptor, hence providing a useful benchmark for their applicability in the endocannabinoid system as well as other G protein-coupled receptors.

METHODS

The study utilized the docked dataset (Induced Fit Docking with Glide XP scoring function) from Loo et al., consisting of 46 ligands-23 agonists and 23 antagonists. The equilibrated structures from Loo et al. were subjected to 30 ns production simulations using GROMACS 2018 at 300 K and 1 atm with the velocity rescaling thermostat and the Parinello-Rahman barostat. AMBER ff99SB*-ILDN was used for the proteins, General Amber Force Field (GAFF) was used for the ligands, and Slipids parameters were used for lipids. MM/PBSA and MM/GBSA binding free energies were then calculated using gmx_MMPBSA. The solute dielectric constant was varied between 1, 2, and 4 to study the effect of different solute dielectric constants on the performance of MM/PB(GB)SA. The effect of entropy on MM/PB(GB)SA binding free energies was evaluated using the interaction entropy module implemented in gmx_MMPBSA. Five GB models, GBHCT, GBOBC1, GBOBC2, GBNeck, and GBNeck2, were evaluated to study the effect of the choice of GB models in the performance of MM/GBSA. Pearson correlation coefficients were used to measure the correlation between experimental and predicted binding free energies.

Insights into the Role of Side-Chain Team Work in nDsbDOx/Red Proteins: Mechanism of Substrate Binding

N-terminal disulfide bond oxidoreductase (nDsbDOx/Red) proteins display divergent substrate binding mechanisms depending on the conformational changes to the Phe70 cap, which is also dependent on the disulfide redox state. In nDsbDOx, the cap dynamics is complex (shows both open/closed Phe70 cap conformations), resulting in an active site that is highly flexible. So the system's active site is conformationally selective (the active site adapts before substrate binding) toward its substrate. In nDsbDRed, the cap is generally closed, resulting in induced fit-type binding (adapts after substrate approach). Recent studies predict Tyr40 and Tyr42 residues to act as internal nucleophiles (Tyr40/42O-) for disulfide association/dissociation in nDsbDOx/Red, supplementing the electron transfer channel. From this perspective, we investigate the cap dynamics and the subsequent substrate binding modes in these proteins. Our molecular dynamics simulations show that the cap opening eliminates Tyr42O- electrostatic interactions irrespective of the disulfide redox state. The active site becomes highly flexible, and the conformational selection mechanism governs. However, Tyr40O- formation does not alter the chemical environment; the cap remains mostly closed and plausibly follows the induced fit mechanism. Thus, it is apparent that mostly Tyr42O- facilitates the internal nucleophile-mediated self-preparation of nDsbDOx/Red proteins for binding.

Gliflozins, sucrose and flavonoids are allosteric activators of lecithin-cholesterol acyltransferase

Lecithin-cholesterol acyltransferase (LCAT) serves as a pivotal enzyme in preserving cholesterol homeostasis via reverse cholesterol transport, a process closely associated with the onset of atherosclerosis. Impaired LCAT function can lead to severe LCAT deficiency disorders for which no pharmacological treatment exists. LCAT-based therapies, such as small molecule positive allosteric modulators (PAMs), against LCAT deficiencies and atherosclerosis hold promise, although their efficacy against atherosclerosis remains challenging. Herein we utilized a quantitative in silico metric to predict the activity of novel PAMs and tested their potencies with in vitro enzymatic assays. As predicted, sodium-glucose cotransporter 2 (SGLT2) inhibitors (gliflozins), sucrose and flavonoids activate LCAT. This has intriguing implications for the mechanism of action of gliflozins, which are commonly used in the treatment of type 2 diabetes, and for the endogenous activation of LCAT. Our results underscore the potential of molecular dynamics simulations in rational drug design.

Applying Spatiotemporal Modeling of Cell Dynamics to Accelerate Drug Development

Cells act as physical computational programs that utilize input signals to orchestrate molecule-level protein-protein interactions (PPIs), generating and responding to forces, ultimately shaping all of the physiological and pathophysiological behaviors. Genome editing and molecule drugs targeting PPIs hold great promise for the treatments of diseases. Linking genes and molecular drugs with protein-performed cellular behaviors is a key yet challenging issue due to the wide range of spatial and temporal scales involved. Building predictive spatiotemporal modeling systems that can describe the dynamic behaviors of cells intervened by genome editing and molecular drugs at the intersection of biology, chemistry, physics, and computer science will greatly accelerate pharmaceutical advances. Here, we review the mechanical roles of cytoskeletal proteins in orchestrating cellular behaviors alongside significant advancements in biophysical modeling while also addressing the limitations in these models. Then, by integrating generative artificial intelligence (AI) with spatiotemporal multiscale biophysical modeling, we propose a computational pipeline for developing virtual cells, which can simulate and evaluate the therapeutic effects of drugs and genome editing technologies on various cell dynamic behaviors and could have broad biomedical applications. Such virtual cell modeling systems might revolutionize modern biomedical engineering by moving most of the painstaking wet-laboratory effort to computer simulations, substantially saving time and alleviating the financial burden for pharmaceutical industries.

Analysis of Glycan Recognition by Concanavalin A Using Absolute Binding Free Energy Calculations

Carbohydrates are key biological mediators of molecular recognition and signaling processes. In this case study, we explore the ability of absolute binding free energy (ABFE) calculations to predict the affinities of a set of five related carbohydrate ligands for the lectin protein, concanavalin A, ranging from 27-atom monosaccharides to a 120-atom complex-type N-linked glycan core pentasaccharide. ABFE calculations quantitatively rank and estimate the affinity of the ligands in relation to microcalorimetry, with a mean signed error in the binding free energy of -0.63 ± 0.04 kcal/mol. Consequently, the diminished binding efficiencies of the larger carbohydrate ligands are closely reproduced: the ligand efficiency values from isothermal titration calorimetry for the glycan core pentasaccharide and its constituent trisaccharide and monosaccharide compounds are respectively -0.14, -0.22, and -0.41 kcal/mol per heavy atom. ABFE calculations predict these ligand efficiencies to be -0.14 ± 0.02, -0.24 ± 0.03, and -0.46 ± 0.06 kcal/mol per heavy atom, respectively. Consequently, the ABFE method correctly identifies the high affinity of the key anchoring mannose residue and the negligible contribution to binding of both β-GlcNAc arms of the pentasaccharide. While challenges remain in sampling the conformation and interactions of these polar, flexible, and weakly bound ligands, we nevertheless find that the ABFE method performs well for this lectin system. The approach shows promise as a quantitative tool for predicting and deconvoluting carbohydrate-protein interactions, with potential application to design of therapeutics, vaccines, and diagnostics.

Discovery of Highly Bioactive Peptides through Hierarchical Structural Information and Molecular Dynamics Simulations

Peptide drugs play an essential role in modern therapeutics, but the computational design of these molecules is hindered by several challenges. Traditional methods like molecular docking and molecular dynamics (MD) simulation, as well as recent deep learning approaches, often face limitations related to computational resource demands, complex binding affinity assessments, extensive data requirements, and poor model interpretability. Here, we introduce PepHiRe, an innovative methodology that utilizes the hierarchical structural information in peptide sequences and employs a novel strategy called Ladderpath, rooted in algorithmic information theory, to rapidly generate and enhance the efficiency and clarity of novel peptide design. We applied PepHiRe to develop BH3-like peptide inhibitors targeting myeloid cell leukemia-1, a protein associated with various cancers. By analyzing just eight known bioactive BH3 peptide sequences, PepHiRe effectively derived a hierarchy of subsequences used to create new BH3-like peptides. These peptides underwent screening through MD simulations, leading to the selection of five candidates for synthesis and subsequent in vitro testing. Experimental results demonstrated that these five peptides possess high inhibitory activity, with IC50 values ranging from 28.13 ± 7.93 to 167.42 ± 22.15 nM. Our study explores a white-box model driven technique and a structured screening pipeline for identifying and generating novel peptides with potential bioactivity.

Molecular Dynamics Unveils Multiple-Site Binding of Inhibitors with Reduced Activity on the Surface of Dihydrofolate Reductase

The sensitivity to protein inhibitors is altered by modifications or protein mutations, as represented by drug resistance. The mode of stable drug binding to the protein pocket has been experimentally clarified. However, the nature of the binding of inhibitors with reduced sensitivity remains unclear at the atomic level. In this study, we analyzed the thermodynamics and kinetics of inhibitor binding to the surface of wild-type and mutant dihydrofolate reductase (DHFR) using molecular dynamics simulations combined with Markov state modeling. A strong inhibitor of methotrexate (MTX) showed a preference for the active site of wild-type DHFR with minimal binding to unrelated (secondary) sites. Deletion of a side-chain fragment in MTX largely destabilized the active site-bound state, with clear evidence of binding to secondary sites. Similarly, the F31V mutation in DHFR diminished the specificity of MTX binding to the active site. These results reveal the presence of multiple-bound states whose stabilities are comparable to or higher than those of the unbound state, suggesting that a reduction in the binding affinity for the active site significantly elevates the fractions of these states. This study presents a theoretical model that more accurately interprets the altered drug sensitivity than the traditional two-state model.

Impairing protein-protein interactions in an essential tRNA modification complex: An innovative antimicrobial strategy against Pseudomonas aeruginosa

Protein-protein interactions (PPIs) have been recognized as a promising target for the development of new drugs, as proved by the growing number of PPI modulators reaching clinical trials. In this context, peptides represent a valid alternative to small molecules, owing to their unique ability to mimic the target protein structure and interact with wider surface areas. Among the possible fields of interest, bacterial PPIs represent an attractive target to face the urgent necessity to fight antibiotic resistance. Growing attention has been paid to the YgjD/YeaZ/YjeE complex responsible for the essential t6A37 tRNA modification in bacteria. We previously identified an α-helix on the surface of Pseudomonas aeruginosa YeaZ, crucial for the YeaZ-YeaZ homodimer formation and the conserved YeaZ-YgjD interactions. Herein, we present our studies for impairing the PPIs involved in the formation of the YeaZ dimers through synthetic peptide derivatives of this helical moiety, both in vitro with purified components and on P. aeruginosa cells. Our results proved the possibility of targeting those PPIs which are usually essential for protein functioning and thus are refractory to mutational changes and antibiotic resistance development.

Immunoinformatics Design of a Multiepitope Vaccine (MEV) Targeting Streptococcus mutans: A Novel Computational Approach

Dental caries, a persistent oral health challenge primarily linked to Streptococcus mutans, extends its implications beyond dental decay, affecting over 4 billion individuals globally. Despite its historical association with childhood, dental caries often persists into adulthood with prevalence rates ranging from 60 to 90% in children and 26 to 85% in adults. Currently, there is a dearth of multiepitope vaccines (MEVs) specifically designed to combat S. mutans. To address this gap, we employed an immunoinformatics approach for MEV design, identifying five promising vaccine candidates (PBP2X, PBP2b, MurG, ATP-F, and AGPAT) based on antigenicity and conservation using several tools including CELLO v.2.5, Vaxign, v2.0, ANTIGENpro, and AllerTop v2.0 tools. Subsequent identification of linear B-cell and T-cell epitopes by SVMTrip and NetCTL/NetMHC II tools, respectively, guided the construction of a MEV comprising 10 Cytotoxic T Lymphocyte (CTL) epitopes, 5 Helper T Lymphocyte (HTL) epitopes, and 5 linear B-cell epitopes, interconnected by suitable linkers. The resultant MEV demonstrated high antigenicity, solubility, and structural stability. In silico immune simulations showcased the MEV's potential to elicit robust humoral and cell-mediated immune responses. Molecular docking studies revealed strong interactions between the MEV construct and Toll-Like Receptors (TLRs) and Major Histocompatibility Complex (MHC) molecules. Remarkably, the MEV-TLR-4 complexes exhibited a low energy score, high binding affinity, and a low dissociation constant. The Molecular Dynamic (MD) simulation analysis suggested that MEV-TLR-4 complexes had the highest stability and minimal conformational changes indicating equilibrium within 40 nanosecond time frames. Comprehensive computational analyses strongly support the potential of the proposed MEV to combat dental caries and associated infections. The study's computational assays yielded promising results, but further validation through in vitro and in vivo experiments is needed to assess its efficacy and safety.

Differentially heterogeneous hydration environment of the familial mutants of α-synuclein

The behavior of hydration water around familial Parkinson's disease linked mutants of α-synuclein may be linked to the early-onset of Parkinson's disease. For the first time, this study compares the local structure and dynamics of hydration water around different segments of some of the natural mutants of α-synuclein, i.e., E46K, G51D, A30P, and A53E, with that of the wild-type protein through explicit water MD simulations. The results show that the C-terminal segments of the fast aggregating mutants such as E46K and A30P are less exposed to water, while those of the slow aggregating ones such as A53E and G51D are more exposed to water relative to that of the wild-type protein. In addition, the water molecules are found to be more ordered around the C-terminal segment of the A53E and G51D mutants as compared to the wild-type protein. This is due to an increase in the overall charge of α-syn upon A53E and G51D mutations. The translational and rotational motions of water molecules in the hydration shell of the C-terminal segment of A53E and G51D mutants are found to be faster relative to that of the wild-type protein. This study validates the differential hydration environment around the C-terminal segment for the causative and protective mutants of α-synuclein.

New approaches for screening grape seed peptides as colourimetric modulators by malvidin-3-O-glucoside stabilisation

The colour of red wine is due to the presence of anthocyanins and their derived pigments, with malvidin-3-O-glucoside being the most predominant. Due to their chemical conformation, anthocyanins are susceptible to several conditions and have limited stability. Through copigmentation processes, anthocyanins can interact non-covalently with other molecules to enhance their stability. As a natural source of proteins and peptides, grape seeds are of particular interest because they may be of significant techno-functional value in the modulation of wine quality characteristics, such as acting as copigments to enhance colour stability. The proposed methodology allowed predicting in-depth insights into the molecular-level nature of interaction between the identified peptides when complexed with malvidin 3-O-glucoside and their colour stabilising properties. Thereby, allowing a prior screening in silico to facilitate their future application in experimental assays, such as obtaining the tested peptides with the characteristics already studied by means of grape seed meal directed hydrolysis.

The D75N and P161S Mutations in the C0-C2 Fragment of cMyBP-C Associated with Hypertrophic Cardiomyopathy Disturb the Thin Filament Activation, Nucleotide Exchange in Myosin, and Actin-Myosin Interaction

About half of the mutations that lead to hypertrophic cardiomyopathy (HCM) occur in the MYBPC3 gene. However, the molecular mechanisms of pathogenicity of point mutations in cardiac myosin-binding protein C (cMyBP-C) remain poorly understood. In this study, we examined the effects of the D75N and P161S substitutions in the C0 and C1 domains of cMyBP-C on the structural and functional properties of the C0-C1-m-C2 fragment (C0-C2). Differential scanning calorimetry revealed that these mutations disorder the tertiary structure of the C0-C2 molecule. Functionally, the D75N mutation reduced the maximum sliding velocity of regulated thin filaments in an in vitro motility assay, while the P161S mutation increased it. Both mutations significantly reduced the calcium sensitivity of the actin-myosin interaction and impaired thin filament activation by cross-bridges. D75N and P161S C0-C2 fragments substantially decreased the sliding velocity of the F-actin-tropomyosin filament. ADP dose-dependently reduced filament sliding velocity in the presence of WT and P161S fragments, but the velocity remained unchanged with the D75N fragment. We suppose that the D75N mutation alters nucleotide exchange kinetics by decreasing ADP affinity to the ATPase pocket and slowing the myosin cycle. Our molecular dynamics simulations mean that the D75N mutation affects myosin S1 function. Both mutations impair cardiac contractility by disrupting thin filament activation. The results offer new insights into the HCM pathogenesis caused by missense mutations in N-terminal domains of cMyBP-C, highlighting the distinct effects of D75N and P161S mutations on cardiac contractile function.

Structural dynamics of the Ca2+-regulated cutinase towards structure-based improvement of PET degradation activity

We previously revealed the structural basis of Ca2+ dependent regulation of a polyethylene terephthalate (PET)-degrading enzyme, Cut190, and proposed a unique reaction cycle in which the enzyme repeatedly binds and releases Ca2+. Here, we report crystal structures of Cut190 mutants with high thermal stability complexed with PET-like ligands that contain aromatic rings. The structural information has allowed us to perform further computational analyses using a PET-trimer bound model. Our multicanonical molecular dynamics simulations and subsequent analyses of the free energy landscapes revealed a novel intermediate form that occurs during the enzymatic reaction cycle. Furthermore, the computational analyses were used to investigate the effect of the point mutations F77L and F81L in the Ca2+-binding site, which showed that the former stabilizes the engaged and open forms to improve transition between the open and active forms, while the latter extremely increases the open form. Subsequent experiments showed that the F77L mutation increased the activity, while the F81L mutation decreased the activity. Our computational analysis has enabled us to explore the dynamics of Cut190 on a completely new level, providing key insights into how the balance between the various conformations influences the reaction cycle and ultimately how to improve the reaction cycle.

Identification of Novel PPARγ Partial Agonists Based on Virtual Screening Strategy: In Silico and In Vitro Experimental Validation

Thiazolidinediones (TZDs) including rosiglitazone and pioglitazone function as peroxisome proliferator-activated receptor gamma (PPARγ) full agonists, which have been known as a class to be among the most effective drugs for the treatment of type 2 diabetes mellitus (T2DM). However, side effects of TZDs such as fluid retention and weight gain are associated with their full agonistic activities toward PPARγ induced by the AF-2 helix-involved "locked" mechanism. Thereby, this study aimed to obtain novel PPARγ partial agonists without direct interaction with the AF-2 helix. Through performing virtual screening of the Targetmol L6000 Natural Product Library and utilizing molecular dynamics (MD) simulation, as well as molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) analysis, four compounds including tubuloside b, podophyllotoxone, endomorphin 1 and paliperidone were identified as potential PPARγ partial agonists. An in vitro TR-FRET competitive binding assay showed podophyllotoxone displayed the optimal binding affinity toward PPARγ among the screened compounds, exhibiting IC50 and ki values of 27.43 µM and 9.86 µM, respectively. Further cell-based transcription assays were conducted and demonstrated podophyllotoxone's weak agonistic activity against PPARγ compared to that of the PPARγ full agonist rosiglitazone. These results collectively demonstrated that podophyllotoxone could serve as a PPARγ partial agonist and might provide a novel candidate for the treatment of various diseases such as T2DM.

Metastasis-Associated Lung Adenocarcinoma Transcript 1 (MALAT1) lncRNA Conformational Dynamics in Complex with RNA-Binding Protein with Serine-Rich Domain 1 (RNPS1) in the Pan-cancer Splicing and Gene Expression

Alternative splicing events increase the transcriptomic and proteomic complexity in cancers. Overexpression of metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), a highly conserved lncRNA, is widely known to promote cancer development, one mechanism for which may be through the regulation of alternative splicing and, thereby, gene expression. Its regulatory interactions with proteins have been a subject of much interest, yet little research has been carried out on the mechanisms adopted. It has been observed that MALAT1 binds to RNA-binding protein with serine-rich domain 1 (RNPS1), being colocalized in the nuclear speckles, and together, these two binding partners may regulate alternative splicing. Upregulated RNPS1 is predicted to play a key role in the pan-cancer development. Experimental tertiary structure of full-length MALAT1 is currently lacking despite the availability of the 3D structure of 3' expression and nuclear retention element. We hypothesize that the computationally modeled tertiary structures of the specific binding motifs in the M-region, E-region, and full-length structures of MALAT1 may adopt a modular structure and bind to the RNPS1 loop region of RS/P domain involved in exon skipping, interacting in a manner fully consistent with the biochemical experiments. Extensive observations using the powerful molecular dynamics (MD) simulations of MALAT1 regions bound to RNPS1 suggested that all three regions form interactive, yet stable complexes. The ranking of the MM-GBSA- and MM-PBSA-derived binding free energies between these complexes corroborated well in the MD simulations and experiments. Energy decomposition analyses suggested that arginines in the RNPS1 protein are among the major contributors toward the binding free energies as calculated by MM-GBSA present in the Amber package; while among the nucleotides, the major contributors were nucleotides with G and A nucleobases, with more contributory effect in comparison to arginines, across the bound M-region, E-region, and full-length MALAT1. This suggests that specific purines play a greater role in the complex formation, in a loop-specific manner, and the more proactive approach in complexation tilts toward MALAT1. To the best of our knowledge, our studies are the first studies taking a unique approach, utilizing the binding motifs to deduce a tertiary structure of MALAT1, toward our understanding of the lncRNA-protein interactions, stability, and binding on a structural basis. The therapeutic implications of targeting this complex formation to regulate splicing and hence, oncogenesis, is further envisaged.

Alchemical Transformations and Beyond: Recent Advances and Real-World Applications of Free Energy Calculations in Drug Discovery

Computational methods constitute efficient strategies for screening and optimizing potential drug molecules. A critical factor in this process is the binding affinity between candidate molecules and targets, quantified as binding free energy. Among various estimation methods, alchemical transformation methods stand out for their theoretical rigor. Despite challenges in force field accuracy and sampling efficiency, advancements in algorithms, software, and hardware have increased the application of free energy perturbation (FEP) calculations in the pharmaceutical industry. Here, we review the practical applications of FEP in drug discovery projects since 2018, covering both ligand-centric and residue-centric transformations. We show that relative binding free energy calculations have steadily achieved chemical accuracy in real-world applications. In addition, we discuss alternative physics-based simulation methods and the incorporation of deep learning into free energy calculations.

Cosolvent Molecular Dynamics Applied to DPP4, DPP8 and DPP9: Reproduction of Important Binding Features and Use in Inhibitor Design

We present our efforts in computational drug design against dipeptidyl peptidase 4 (DPP4), DPP8 and DPP9. We applied cosolvent molecular dynamics (MD) simulations to these three protein targets of interest. Our primary motivation is the growing interest in DPP8 and DPP9 as emerging drug targets. Due to the high similarity between DPP4, DPP8 and DPP9, DPP4 was also included in these analyses. The cosolvent molecular dynamics simulations reproduce key ligand binding features and known binding pockets, while also highlighting interesting fragment positions for future ligand optimization. The resulting fragment maps from the cosolvent molecular dynamics are freely available for use in future research (https://github.com/UAMC-Olivier/DPP489_cosolvent_MD/). Detailed instructions for easy visualization of the fragment maps are provided, ensuring that the results are usable by both computational and medicinal chemists. Additionally, we used the fragment maps to search for the binding pockets with significant potential using an algorithmic approach combining top fragment locations. To discover novel binding scaffolds, a limited pharmacophore screening was performed, where the pharmacophores were based on the analyses of the cosolvent simulations. Unfortunately, inhibitory potencies were in the higher micromolar range, but we optimized the resulting scaffolds in silico using relative binding free energy calculations for future inhibitor design and synthesis.

Investigating the role of PmrB mutation on Colistin antibiotics drug resistance in Klebsiella Pneumoniae

Klebsiella pneumoniae, a member of the Enterobacteriaceae family, naturally resides in the digestive tracts of both healthy animals and humans. Carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a significant health risk for hospitalized patients worldwide, greatly reducing the effectiveness of commonly used antibiotics. This leaves healthcare providers with limited treatment options, often relying on colistin. PmrB is important for the survival of Klebsiella pneumonia and, a mutation in the PmrB protein is accountable for the development of colistin antibiotic resistance in Klebsiella pneumonia. This is especially important because colistin is a fundamental component in the treatment of pneumonia. Three mutated residues-T157P, G207D, and T246A-are responsible for colistin resistance. The structural alterations and underlying mechanisms in the PmrB protein that cause resistance owing to mutation remain unclear. As a result, this study is focused to the exploration of the putative mechanism of resistance resulting from these mutations, as well as the structure modification of normal and mutant PmrB proteins, using molecular docking and molecular dynamics simulations analysis. Our results demonstrated that the interaction paradigm for the mutants has been altered and thus showing a significant effect upon the hydrogen bonding network. Interestingly, the binding of Colistin with the three mutant demonstrate unstable behavior as compared with WT+Colistin. The proposed drug-resistance mechanism will help to guide the development of PmrB drugs. These finding may give a new framework for developing novel drugs against the mutant version of PmrB.

Alpha-glucosidase inhibitory compounds from Vietnamese lichen Usnea baileyi: in vitro and in silico aspects

Using a bio-guided isolation on the Vietnamese lichen Usnea baileyi based on alpha-glucosidase inhibition, eleven compounds were isolated and structurally elucidated, namely, protocetraric acid (1), 8'-methylstictic acid (2), stictic acid (3), 4,6-diformyl-8-hydroxy-3-methoxy-1,9-dimethyl-11-oxo-11H-dibenzo[b,e][1,4]dioxepine-7-carboxylic acid (4), vicanicin (5), norstictic acid (6), diffractaic acid (7), barbatic acid (8), atranol (9), 5-chlorohaematommic acid (10), and eumitrin A1 (11). Their chemical structures were identified by extensive 1D and 2D NMR analysis and high-resolution mass spectroscopy and compared with those reported in literature. Protocetraric acid (1) and norstictic acid (6) were selected for further modification to derive new compounds, namely, 1a-1e and 6a. Both isolated and synthesized compounds were assessed for their alpha-glucosidase inhibitory activity. Compounds 1-6, 1a-1e, 6a, and 11 showed significant alpha-glucosidase inhibition with IC50 values ranging from 10.4 to 130 μM. Molecular docking was applied to the most active compounds 1-3, 6, 1a-1e, and 6a to clarify the inhibitory mechanism. Compound 1e was determined to be a mixed inhibitor through a kinetic study.

Unraveling the orientation of an enzyme adsorbed onto a metal-organic framework

Bio-conversion of lignocellulosic biomass to bioethanol fuel is a highly desirable yet challenging objective because of the low catalytic activity and high cost of β-glucosidase (BGL). Recently, ZIF-8, an emerging organic porous material, has been proposed as a promising candidate for enzyme immobilization to improve associated activity and stability. However, the underlying interaction mechanism of binding BGL on the ZIF-8 surface is yet to be clarified. Here, the adsorption of BGL onto ZIF-8 is explored for the first time by molecular dynamics simulations. The results show that BGL adsorbs on the ZIF-8 surface with a "back-on" orientation. The adsorption free energy analysis shows that the adsorption process is enthalpy driven. In addition, the electrostatic interaction between negatively charged residues and Zn2+ on the surface of ZIF-8 is found to play a decisive role in surface binding, which accounts for 98% of the total interaction energy. The secondary structure of BGL is not affected despite the strong adsorption, suggesting the good biocompatibility of ZIF-8. This study not only provides a reliable theoretical insight into understanding the interaction mechanism between BGL and ZIF-8, but also helps the rational design of ZIF-8-based materials for bio-related applications.

Investigation of the molecular interaction between apraclonidine, an α2-adrenergic receptor agonist, and bovine serum albumin using fluorescence and molecular docking techniques

Apraclonidine (APR) is a potent and selective α2-adrenergic receptor agonist used in the diagnosis of Horner's Syndrome, and the residuals of APR that accumulate in tissues of animals can cause central nervous and cardiovascular systems influences in humans. Therefore, to understand the influence of APR on human health, we examined the interaction of APR with the carrier protein in plasma, bovine serum albumin (BSA). The BSA fluorescence signal was quenched due to the APU-BSA complex formation and a weak binding affinity was estimated between APR and BSA. The inclusion of fluorescence, UV-vis absorption, molecular docking, and dynamics simulation techniques employed to broadly investigate the combination of APR with BSA at typical physiological conditions. The thermodynamic results revealed that enthalpy (ΔH0) and entropy (ΔS0) changes were computed as +11.14 kJ mol-1 and +97.56 J mol-1 K-1, respectively, which represented the binding is principally entropy-driven and the hydrophobic forces acting a significant role in the reaction. Analysis of synchronous and 3-D fluorescence signals revealed microenvironmental variations close to BSA's Trp and Tyr residues upon APR addition. Both the competitive site marker as well as molecular docking results detected that APR exhibited a stronger binding affinity towards Drug Site 2 (DS2) compared to Drug Site 1 (DS1).

Computer-Aided Site-Specific PEGylation of PET Hydrolases for Enhanced PET Degradation

The enormous accumulation of poly(ethylene terephthalate) (PET) waste has posed a serious threat to the environment and human health, and biodegradation with PET hydrolase (PETase) can be a possible solution. Herein, we propose site-specifically modifying PETase with amphiphilic polymers to improve the enzyme performance at ambient temperature. For this purpose, we devise a computer-aided strategy to prioritize the conjugation site, and polyethylene glycol (PEG) preparations of 0.55 to 10 kDa are site-specifically conjugated to PETase. The most active conjugate PETase-PEG 5k (PETase-5K) shows an increase of melting temperature (3.88 °C) and significantly improves PET degradation performance (3.5- and 3.1-fold increases at 30 and 40 °C, respectively). Experimental investigation and molecular dynamics simulations reveal that the site-specific PEGylation increases the hydrophobic solvent-accessible surface area and the binding capability to the PET surface, thickens the hydration layer, increases the intramolecular hydrogen bonding, reduces the interactions between water and the conjugated enzyme surface, and rigidifies the enzyme structure via hydrogen bonding and hydrophobic interactions between the polymer and the enzyme, thus leading to improved enzymatic performance of PETase-5K. We further validate the versatility of the site-specific PEGylation in one of the most evolved variants of PETase, FAST-PETase, by 1.8-fold improvement in PET degradation at 30 °C. The presented computer-aided site-specific conjugation strategy has opened a new avenue to enhancing PETase performance at ambient temperature, and the contribution of PEGylation to PETase unraveled in this work laid a foundation for the rational engineering of PET hydrolases.

Resolving the Structure of a Guanine Quadruplex in TMPRSS2 Messenger RNA by Circular Dichroism and Molecular Modeling

The presence of a guanine quadruplex in the opening reading frame of the messenger RNA coding for the transmembrane serine protease 2 (TMPRSS2) may pave the way to original anticancer and host-oriented antiviral strategy. Indeed, TMPRSS2 in addition to being overexpressed in different cancer types, is also related to the infection of respiratory viruses, including SARS-CoV-2, by promoting the cellular and viral membrane fusion through its proteolytic activity. The design of selective ligands targeting TMPRSS2 messenger RNA requires a detailed knowledge, at atomic level, of its structure. Therefore, we have used an original experimental-computational protocol to predict the first resolved structure of the parallel guanine quadruplex secondary structure in the RNA of TMPRSS2, which shows a rigid core flanked by a flexible loop. This represents the first atomic scale structure of the guanine quadruplex structure present in TMPRSS2 messenger RNA.