Molecular Dynamics Simulation Approach Research Articles

Structural insights into non-hotspot KRAS mutations and their potential as targets for effective cancer therapies

Kirsten rat sarcoma virus protein (KRAS) is a protein that plays a central role in signal transduction using extracellular signal regulated kinase (ERK) and mitogen activated protein kinase (MAPK) cellular signaling pathway. KRAS is a frequently mutated oncogene and plays a pivotal role in tumor initiation and progression. Hotspot mutations on codon 12, 13 and 61 in KRAS are well-known for their role in drug resistance and non-hotspot mutations also play a significant part in contributing to resistance mechanisms. The understanding of how these non-hotspot mutations might affect the signal transduction of KRAS and their contribution towards drug resistance is understudied. Here we provide structural insights into the interaction of non-hotspot KRAS mutants with GTP (the native ligand) using a molecular docking and molecular dynamics simulation approach. Extensive molecular docking and simulation studies suggest that non-hotspot mutations (E31D and E63K) show stable interaction with native ligand using all five trajectories, as evidenced by root mean square of distance (RMSD), root mean square of fluctuation (RMSF), radius of gyration (RoG), coulomb short-range energy and MMGBSA analysis. These results suggest that non-hotspot mutations do not undermine the oncogenic nature of KRAS. This observation is consistent with previous findings where overexpressing E31D and E63K mutations share phenotypic features with G12D and G13D transfected cells, including increased proliferative capacity, actin cytoskeleton organization, and migration rates. We further test whether FDA-approved KRAS inhibitors sotorasib and adagrasib successfully inhibit the E31D and E63K mutants. Results suggest that these two non-hotspot mutants can be inhibited by both drugs with following trend of structural stability (E31D > E63K > wild-KRAS > Q61H > G12C). Based on sharp coherence in trajectories between wild KRAS and non-hotspot mutants, it is suggested that these novel mutants do not contribute to drug resistance mechanism. Overall, we provide a comprehensive understanding of the impact of non-hotspot mutations on KRAS and their potential as targets for effective cancer therapies. Communicated by Ramaswamy H. Sarma

Molecular mechanisms of chaperone-directed protein folding: Insights from atomistic simulations.

Molecular chaperones, a family of proteins of which Hsp90 and Hsp70 are integral members, form an essential machinery to maintain healthy proteomes by controlling the folding and activation of a plethora of substrate client proteins. This is achieved through cycles in which Hsp90 and Hsp70, regulated by task-specific co-chaperones, process ATP and become part of a complex network that undergoes extensive compositional and conformational variations. Despite impressive advances in structural knowledge, the mechanisms that regulate the dynamics of functional assemblies, their response to nucleotides, and their relevance for client remodeling are still elusive. Here, we focus on the glucocorticoid receptor (GR):Hsp90:Hsp70:co-chaperone Hop client-loading and the GR:Hsp90:co-chaperone p23 client-maturation complexes, key assemblies in the folding cycle of glucocorticoid receptor (GR), a client strictly dependent upon Hsp90/Hsp70 for activity. Using a combination of molecular dynamics simulation approaches, we unveil with unprecedented detail the mechanisms that underpin function in these chaperone machineries. Specifically, we dissect the processes by which the nucleotide-encoded message is relayed to the client and how the distinct partners of the assemblies cooperate to (pre)organize partially folded GR during Loading and Maturation. We show how different ligand states determine distinct dynamic profiles for the functional interfaces defining the interactions in the complexes and modulate their overall flexibility to facilitate progress along the chaperone cycle. Finally, we also show that the GR regions engaged by the chaperone machinery display peculiar energetic signatures in the folded state, which enhance the probability of partial unfolding fluctuations. From these results, we propose a model where a dynamic cross-talk emerges between the chaperone dynamics states and remodeling of client-interacting regions. This factor, coupled to the highly dynamic nature of the assemblies and the conformational heterogeneity of their interactions, provides the basis for regulating the functions of distinct assemblies during the chaperoning cycle.

Raman spectroscopy study of 7,8-dihydrofolate inhibition on the Wuhan strain SARS-CoV-2 binding to human ACE2 receptor

Emerging evidence suggests that elevated levels of folic acid in the bloodstream may confer protection against Wuhan-SARS-CoV-2 infection and mitigate its associated symptoms. Notably, two comprehensive studies of COVID-19 patients in Israel and UK uncovered a remarkable trend, wherein individuals with heightened folic acid levels exhibited only mild symptoms and necessitated no ventilatory support. In parallel, research has underscored the potential connection between decreased folic acid levels and the severity of Covid-19 among hospitalized patients. Yet, the underlying mechanisms governing this intriguing inhibition remain elusive. In a quest to elucidate these mechanisms, we conducted a molecular dynamics simulation approach followed by a Raman spectroscopy study to delve into the intricate interplay between the folic acid metabolite, 7,8-dihydrofolate (DHF), and the angiotensin-converting enzyme ACE2 receptor, coupled with its interaction with the receptor-binding domain (RBD) of the Wuhan strain of SARS-CoV-2. Through a meticulous exploration, we scrutinized the transformation of the ACE2 + RBD complex, allowing these reactants to form bonds. This was juxtaposed with a similar investigation where ACE2 was initially permitted to react with DHF, followed by the exposure of the ACE2 + DHF complex to RBD. We find that DHF, when bonded to ACE2, functions as a physical barrier, effectively inhibiting the binding of the Wuhan strain RBD. This physicochemical process offers a cogent explanation for the observed inhibition of host cell infection in subjects receiving supplementary folic acid doses, as epidemiologically substantiated in multiple studies. This study not only sheds light on a potential avenue for mitigating SARS-CoV-2 infection but also underscores the crucial role of folic acid metabolites in host-virus interactions. This research paves the way for novel therapeutic strategies in the battle against COVID-19 and reinforces the significance of investigating the molecular mechanisms underlying the protective effects of folic acid in the context of viral infections.

Magnesium Ion Gated Ion Rejection through Carboxylated Graphene Oxide Nanopore: A Theoretical Study.

While nanoporous graphene oxide (GO) is recognized as one of the most promising reverse osmosis desalination membranes, limited attention has been paid to controlling desalination performance through the large GO pores, primarily due to significant ion leakage resulting in the suboptimal performance of these pores. In this study, we employed a molecular dynamics simulation approach to demonstrate that Mg2+ ions, adhered to carboxylated GO nanopores, can function as gates, regulating the transport of ions (Na+ and Cl-) through the porous GO membrane. Specifically, the presence of divalent cations near a nanopore reduces the concentration of salt ions in the vicinity of the pore and prolongs their permeation time across the pore. This subsequently leads to a notable enhancement in salt rejection rates. Additionally, the ion rejection rate increases with more adsorbed Mg2+ ions. However, the presence of the adsorbed Mg2+ ions compromises water transport. Here, we also elucidate the impact of graphene oxidation degree on desalination. Furthermore, we design an optimal combination of adsorbed Mg2+ ion quantity and oxidation degree to achieve high water flux and salt rejection rates. This work provides valuable insights for developing new nanoporous graphene oxide membranes for controlled water desalination.

Multiscale Molecular Dynamics Simulations of an Active Self-Assembling Material.

Inspired by the adaptability observed in biological materials, self-assembly processes have attracted significant interest for their potential to yield novel materials with unique properties. However, experimental methods have often fallen short in capturing the molecular details of the assembly process. In this study, we employ a multiscale molecular dynamics simulation approach, complemented by NMR quantification, to investigate the mechanism of self-assembly in a redox-fueled bioinspired system. Contrary to conventional assumptions, we have uncovered a significant role played by the monomer precursor in the assembly process, with its presence varying with concentration and the extent of conversion of the monomer to the dimer. Experimental confirmation through NMR quantification underscores the concentration-dependent incorporation of monomers into the fibrous structures. Furthermore, our simulations also shed light on the diverse intermolecular interactions, including T-shaped and parallel π stacking, as well as hydrogen bonds, in stabilizing the aggregates. Overall, the open conformation of the dimer is preferred within these aggregates. However, inside the aggregates, the distribution of conformations shifts slightly to the closed conformation compared to on the surface. These findings contribute to the growing field of bioinspired materials science by providing valuable mechanistic and structural insights to guide the design and development of self-assembling materials with biomimetic functionalities.

In silico exploration of the potential inhibitory activities of in-house and ZINC database lead compounds against alpha-glucosidase using structure-based virtual screening and molecular dynamics simulation approach

Inhibitors of α-glucosidase have been used to treat type-2 diabetes (T2DM) by preventing the breakdown of carbohydrates into glucose and prevent enhancing glucose conversion. Structure-based virtual screening (SBVS) was used to generate novel chemical scaffold-ligand α-glucosidase inhibitors. The databases were screened against the receptor α-glucosidase using SBVS and molecular dynamics simulation (MDS) techniques in this study. Based on molecular docking studies, three and two compounds of α-glucosidase inhibitors were chosen from a commercial database (ZINC) and an In-house database for this study respectively. The mode of binding interactions of the selected compounds later predicted their α-glucosidase inhibitory potential. Finally, one out of three lead compound from ZINC and one out of two lead compound from In-house database were shortlisted based on interactions. Furthermore, MDS and post-MDS strategies were used to refine and validate the shortlisted leads along with the reference acarbose/α-glucosidase. The Hits’ ability to inhibit α-glucosidase was predicted by SBVS, indicating that these compounds have good inhibitory activities. The lead inhibitor’s structure may serve as templates for the design of novel inhibitors, and in vitro testing to confirm their anti-diabetic potential is necessary. These insights can help rationally design new effective anti-diabetic drugs. Communicated by Ramaswamy H. Sarma

Secondary metabolites of Trichoderma spp. as EGFR tyrosine kinase inhibitors: Evaluation of anticancer efficacy through computational approach.

The present study explores the epidermal growth factor receptor (EGFR) tyrosine kinase inhibition efficacy of secondary metabolites in Trichoderma spp. through molecular docking, molecular dynamics (MD) simulation and MM-PBSA approach. The result of molecular docking confirmed that out of 200 metabolites screened, three metabolites such as Harzianelactone A, Pretrichodermamide G and Aspochalasin M, potentially bound with the active binding site of EGFR tyrosine kinase domain(PDB ID: 1M17) with a threshold docking score of ≤- 9.0 kcal/mol when compared with the standard EGFR inhibitor (Erlotinib). The MD simulation was run to investigate the potential for stable complex formation in EGFR tyrosine kinase domain-unbound/lead metabolite (Aspochalasin M)-bound/standard inhibitor (Erlotinib)-bound complex. The MD simulation analysis at 100 ns revealed that Aspochalasin M formed the stable complex with EGFR. Besides, the in silico predication of pharmacokinetic properties further confirmed that Aspochalasin M qualified the drug-likeness rules with no harmful side effects (viz., hERG toxicity, hepatotoxicity and skin sensitization), non-mutagenicity and favourable logBB value. Moreover, the BOILED-Egg model predicted that Aspochalasin M showed a higher gastrointestinal absorption with improved bioavailability when administered orally and removed from the central nervous system (CNS). The results of the computational studies concluded that Aspochalasin M possessed significant efficacy in binding EGFR's active sites compared to the known standard inhibitor (Erlotinib). Therefore, Aspochalasin M can be used as a possible anticancer drug candidate and further in vitro and in vivo experimental validation of Aspochalasin M of Trichoderma spp. are required to determine its anticancer potential.

Identification of antiviral phytochemicals from cranberry as potential inhibitors of SARS-CoV-2 main protease (Mpro)

Cranberry phytochemicals are known to possess antiviral activities. In the current study, we explored the therapeutic potential of cranberry against SARS-CoV-2 by targeting its main protease (Mpro) enzyme. Firstly, phytochemicals of cranberry origin were identified from three independent databases. Subsequently, virtual screening, using molecular docking and molecular dynamics simulation approaches, led to the identification of three lead phytochemicals namely, cyanidin 3-O-galactoside, β-carotene and epicatechin. Furthermore, in vitro enzymatic assays revealed that cyanidin 3-O-galactoside had the highest inhibitory potential with IC50 of 9.98 μM compared to the other two phytochemicals. Cyanidin 3-O-galactoside belongs to the class of anthocyanins. Anthocyanins extracted from frozen cranberry also exhibited the highest inhibitory potential with IC50 of 23.58 μg/ml compared to the extracts of carotenoids and flavanols, the class for β-carotene and epicatechin, respectively. Finally, we confirm the presence of the phytochemicals in the cranberry extracts using targeted LC-MS/MS analysis. Our results, therefore, indicate that the identified cranberry-derived bioactive compounds as well as cranberry could be used for therapeutic interventions against SARS-CoV-2.

Study the solubility of pharmaceutical ingredients and their eutectic mixtures: An in-depth density functional theory and molecular dynamics simulations approaches

Solubility is a major concern for many active pharmaceutical ingredients (APIs) and drugs. Owing to their better solubility, biodegradability and low toxicity of APIs and drugs, eutectic mixtures are emerging as the system to enhance their solubility with no loss of biological activity. In the present work, authors have taken camizestrant, deucravacitinib, and iclepertin as the active pharmaceutical ingredients (API) because they have poor solubility in water. Authors have designed eutectic mixtures (EMs) of the selected APIs with the amino acids (aspartic acid, lysine, phenylalanine, and proline) and studied for their physiochemical properties in default and water using density functional theory calculations, performed by Gaussian. The solubility of the APIs, amino acids and the designed eutectic mixtures of APIs have been determined and discussed using the dipole moment. The results showed that the solubility of the designed eutectic mixtures have better aqueous solubility than the APIs alone. Further, molecular dynamics (MD) simulations were done for APIs and EMs to study their stability and interactions.

Integrating molecular docking and molecular dynamics simulation approaches for the investigation of the affinity and interactions of curcumin with Class D β-lactamase

ntroduction: Antimicrobial resistance has become major concern of treating infectious disease due to their extensive use, which led to bacterial gen modification and secretion of some enzymes by these microorganisms that make them survival despite the presence of antibiotics. Searching of inhibitors for these resistant pathogens were helpful to elevate the impact of antibiotics in curing diseases. Curcumin is a natural compound which has several medicinal effects, can be used to inhibit OXA-10 β-lactamase class D enzymes. Materials and Methods: Molecular docking and Molecular dynamic simulation utilized to understand the binding pose, structural integrity, stability and binding energy of class D beta lactamase with Curcumin using Autodock 4.2.2 software and GROMACS 2019.6 program applying AMBER99SB force field respectively. Results: Molecular docking results and interaction analysis of molecular dynamics simulations indicated stable hydrogen bonds and van der Waals interactions of Curcumin with OXA-10 β-lactamase. Conclusion: This paper indicates that curcumin which is a natural ingredient can be used as a potential inhibitor of class D β -lactamase OXA-10.

Integrating molecular docking and molecular dynamics simulation approaches for investigation of the affinity and interactions of Berberine with Class C β-Lactamase

Background: Antibiotic resistance is a significant health concern, as bacteria produce enzymes that inhibit antimicrobial drug activity, increasing disease generation. This study investigates the inhibitory effect of berberine on β-lactamase enzyme activity and antibiotic effectiveness. Methods: Molecular docking was utilized to find the binding pose and binding affinity of a new inhibitory ligand with the AmpC enzyme using Autodock software version 4.2.2. MD simulations were performed in free form and complicated to understand the stability of the protein-ligand docked complex. Results: The molecular docking result indicated the proper interaction between berberine and the AmpC β-lactamase enzyme with a suitable binding pose and binding energy of -6.55 kcal/mol. The MD simulation of systems verifies the docking result, which shows stable hydrogen bonds of berberine with AmpC and good equivalence between RMSD, RMSF, SASA, etc. Conclusion: This paper reveals that berberine, which is a natural ingredient with multiple medicinal characteristics, can be applied as a potential inhibitor of class C β-lactamase AmpC. Hence, the outcome of the calculations performed provides valuable data to design new inhibitors with therapeutic potential to control the β-lactamase activity.

Effect of Solute on Interfacial Properties and Micelle Structure of Dodecylbenzenesulfonate (DBS): Experimental and Molecular Dynamics Studies.

A combined experimental and molecular dynamic simulation approach was used to examine the structure and interfacial properties of solute-saturated micelles. The properties of dodecylbenzenesulfonate (DBS) micelles were examined in dodecane and benzene hydrocarbon systems. Pyrene fluorescence was used to determine the aggregation number of surfactant monomers in the micelle systems. Molecular dynamic (MD) simulations using energy minimization applying the CHARMm force field with the TIP3P model for water. Comparison of the DBS/benzene and DBS/Dodecane micelles equilibrium structures via radial distribution function (RDF) and probability distribution function (PDF) analysis indicates that the area per head group for the DBS/Benzene micelle interface is significantly larger than that of the DBS/Dodecane at the interface. It was also determined that benzene molecules can move freely within the micelle while dodecane is strictly confined in the core of the micelle. The increased interfacial area per monomer caused by the insertion of benzene also reduces the effectiveness of the surfactant, which has implications for use in various environmental applications. However, the DBS/benzene micelle can solubilize many more hydrocarbon molecules in one micelle with less surfactant monomer (i.e., lower aggregation number) per micelle due to the increased available packing positions within the micelle. This, in turn, increases the efficiency of the surfactant in real-world applications which is consistent with previous laboratory results. Understanding the differing solubilization characteristics of surfactants against various classes of hydrocarbons in single solute systems is a necessary step to beginning to understand their solubilization properties in the mixed waste systems prevalent in most surfactant enhanced remediation (SEAR) strategies.

Evaluation and comparison of the mechanism of two bioactive materials in vital pulp therapy: a molecular dynamics simulation approach

Evaluation and comparison of the mechanism of two bioactive materials in vital pulp therapy: a molecular dynamics simulation approach

Hygroscopic Growth of Adsorbed Water Films on Smectite Clay Particles.

Hygroscopic growth of adsorbed water films on clay particles underlies a number of environmental science questions, from the air quality and climate impacts of mineral dust aerosols to the hydrology and mechanics of unsaturated soils and sedimentary rocks. Here, we use molecular dynamics (MD) simulations to establish the relation between adsorbed water film thickness (h) and relative humidity (RH) or disjoining pressure (Π), which has long been uncertain due to factors including sensitivity to particle shape, surface roughness, and aqueous chemistry. We present a new MD simulation approach that enables precise quantification of Π in films up to six water monolayers thick. We find that the hygroscopicity of phyllosilicate mineral surfaces increases in the order mica < K-smectite < Na-smectite. The relationship between Π and h on clay surfaces follows a double exponential decay with e-folding lengths of 2.3 and 7.5 Å. The two decay length scales are attributed to hydration repulsion and osmotic phenomena in the electrical double layer (EDL) at the clay-water interface.

Comprehensive characterization of coding and non-coding single nucleotide polymorphisms of the Myoneurin (MYNN) gene using molecular dynamics simulation and docking approaches.

Genome-wide association studies (GWAS) identified a coding single nucleotide polymorphism, MYNN rs10936599, at chromosome 3q. MYNN gene encodes myoneurin protein, which has been associated with several cancer pathogenesis and disease development processes. However, there needed to be a more detailed characterization of this polymorphism's (and other coding and non-coding polymorphisms) structural, functional, and molecular impact. The current study addressed this gap and analyzed different properties of rs10936599 and non-coding SNPs of MYNN via a thorough computational method. The variant, rs10936599, was predicted functionally deleterious by nine functionality prediction approaches, like SIFT, PolyPhen-2, and REVEL, etc. Following that, structural modifications were estimated through the HOPE server and Mutation3D. Moreover, the mutation was found in a conserved and active residue, according to ConSurf and CPORT. Further, the secondary structures were predicted, followed by tertiary structures, and there was a significant deviation between the native and variant models. Similarly, molecular simulation also showed considerable differences in the dynamic pattern of the wildtype and mutant structures. Molecular docking revealed that the variant binds with better docking scores with ligand NOTCH2. In addition to that, non-coding SNPs located at the MYNN locus were retrieved from the ENSEMBL database. These were found to disrupt the transcription factor binding regulatory regions; nonetheless, only two affect miRNA target sites. Again, eight non-coding variants were detected in the testes with normalized expression, whereas HaploReg v4.1 unveiled annotations for non-coding variants. In summary, in silico comprehensive characterization of coding and non-coding single nucleotide polymorphisms of MYNN gene will assist researchers to work on MYNN gene and establish their association with certain types of cancers.

Assessing Inhibitory potential of natural compounds against BACE1 in Alzheimer's disease: A molecular docking and molecular dynamics simulation approach

Assessing Inhibitory potential of natural compounds against BACE1 in Alzheimer's disease: A molecular docking and molecular dynamics simulation approach

Structure-based screening of FDA-approved drugs identifies potential histone deacetylase 3 repurposed inhibitor: molecular docking and molecular dynamic simulation approaches.

Histone deacetylase 3 (HDAC3) is a member of the histone deacetylase family that has emerged as a crucial target in the quest for novel therapeutic interventions against various complex diseases, including cancer. The repositioning of FDA-approved drugs presents a promising avenue for the rapid discovery of potential HDAC3 inhibitors. In this study, we performed a structure-based virtual screening of FDA-approved drugs obtained from DrugBank. Candidate hits were selected based on their binding affinities and interactions with HDAC3. These promising hits were then subjected to a comprehensive assessment of their biological properties and drug profiles. Our investigation identified two FDA-approved drugs, Imatinib and Carpipramine, characterized by their exceptional affinity and specificity for the binding pocket of HDAC3. These molecules demonstrated a strong preference for HDAC3 binding site and formed interactions with functionally significant residues within the active site pocket. To gain deeper insights into the binding dynamics, structural stability, and interaction mechanisms, we performed molecular dynamics (MD) simulations spanning 300nanoseconds (ns). The results of MD simulations indicated that Imatinib and Carpipramine stabilized the structure of HDAC3 and induced fewer conformational changes. Taken together, the findings from this study suggest that Imatinib and Carpipramine may offer significant therapeutic potential for treating complex diseases, especially cancer.

Insight into molecular structures and dynamical properties of niosome bilayers containing melatonin molecules: a molecular dynamics simulation approach.

Niosomes represent vesicular carriers capable of encapsulating both hydrophobic and hydrophilic drugs within their inner core or bilayer shell. They are typically composed of non-ionic synthetic surfactants such as sorbitan monostearate (Span60) with the addition of cholesterol (Chol). The physical properties and stability of niosomal vesicles strongly depend on the composition of their bilayers, which plays a significant role in determining the efficiency of drug encapsulation and release in drug delivery systems. In this study, we have explored the interactions between melatonin (Mel) molecules and the niosome bilayer, as well as their resulting physical properties. Molecular dynamics simulations were employed to investigate melatonin-inserted niosome bilayers, both with and without the inclusion of cholesterol. The simulation results revealed that cholesterol notably influences the location of melatonin molecules within the niosome bilayers. In the absence of cholesterol, melatonin tends to occupy the region around the Span60 tail groups. However, in the presence of cholesterol, melatonin is found in the vicinity of the Span60 head groups. Melatonin molecules in niosome bilayers without cholesterol exhibit a more ordered orientation when compared to those in bilayers containing 50 mol% cholesterol. The bilayer structure of the Span60/Mel and Span60/Chol/Mel systems exhibited a liquid-disordered phase (Ld). In contrast, the Span60/Chol bilayer system displays a liquid-ordered phase (Lo) with less fluidity. This study reveals that melatonin induces a disorderly bilayer structure and greater lateral expansion, whereas cholesterol induces an orderly bilayer structure and a more condensed effect. Cholesterol plays a crucial role in condensing the bilayer structure with stronger interactions between Span60 and cholesterol. The addition of 50 mol% cholesterol in the Span60 bilayers not only enhances the stability and rigidity of niosomes but also facilitates the easier release of melatonin from the bilayer membranes. This finding is particularly valuable in the context of preparing niosomes for drug delivery systems.

EFFICIENT SYNTHESIS OF 1-(BROMOMETHYL)-3,5-DIMETHOXYBENZENE: X-RAY STRUCTURE, HIRSHFELD SURFACE ANALYSIS, DFTs, AND MOLECULAR MODELLING INVESTIGATIONS AS TYROSINASE INHIBITOR

The synthesis of 1-(bromomethyl)-3,5-dimethoxybenzene, a crucial intermediate in the formation of various natural products, was carried out through a straightforward three-step procedure starting from 3,5-dihydroxybenzoic acid. The structure of the synthesized derivative was fully characterized using a combination of spectroscopic techniques and single crystal X-ray diffraction. The crystalline sample was found to possess monoclinic symmetry with dimensions a = 8.4054(10) Å, b = 4.4245(6) Å, c = 25.016(3) Å, volume V = 928.9(2) Å3 and Z = 4.0. In order to assess the inhibitory potential of the synthesized crystal, a comprehensive in-silico investigation was conducted which involved molecular docking, density function theory (DFT) analysis, and molecular dynamics (MD) simulation studies. The docking analysis was utilized to determine the binding orientation of the compound with respect to the target proteins, while DFT analysis was utilized to evaluate the molecule’s reactivity profile. The MD simulation approach was used to evaluate the structural rearrangements and chemical interactions that occurred during the simulation period. The results of these studies suggest that the synthesized crystal could potentially serve as a dual inhibitor of RNR and tyrosinase and could be a suitable candidate for the synthesis of noval anti-cancer agent for the treatment of associated malignancies.

ROS1 kinase inhibition reimagined: identifying repurposed drug via virtual screening and molecular dynamics simulations for cancer therapeutics.

Precision medicine has revolutionized modern cancer therapeutic management by targeting specific molecular aberrations responsible for the onset and progression of tumorigenesis. ROS proto-oncogene 1 (ROS1) is a receptor tyrosine kinase (RTK) that can induce tumorigenesis through various signaling pathways, such as cell proliferation, survival, migration, and metastasis. It has emerged as a promising therapeutic target in various cancer types. However, there is very limited availability of specific ROS1 inhibitors for therapeutic purposes. Exploring repurposed drugs for rapid and effective treatment is a useful approach. In this study, we utilized an integrated approach of virtual screening and molecular dynamics (MD) simulations of repurposing existing drugs for ROS1 kinase inhibition. Using a curated library of 3648 FDA-approved drugs, virtual screening identified drugs capable of binding to ROS1 kinase domain. The results unveil two hits, Midostaurin and Alectinib with favorable binding profiles and stable interactions with the active site residues of ROS1. These hits were subjected to stability assessment through all-atom MD simulations for 200 ns. MD results showed that Midostaurin and Alectinib were stable with ROS1. Taken together, the study showed a rational framework for the selection of repurposed Midostaurin and Alectinib with ROS1 inhibitory potential for therapeutic management after further validation.