MM-GBSA Calculations Research Articles

Discovery of potent DNMT1 inhibitors against sickle cell disease using structural-based virtual screening, MM-GBSA and molecular dynamics simulation-based approaches

Sickle cell disease (SCD) is an autosomal recessive genetic disorder affecting millions of people worldwide. A reversible and selective DNMT1 inhibitor, GSK3482364, has been known to decrease the overall methylation activity of DNMT1, resulting in the increase of HbF levels and percentage of HbF-expressing erythrocytes in an in vitro and in vivo model. In this study, a structure-based virtual screening was done with GSK3685032, a co-crystalized ligand of DNMT1 (PDB ID: 6X9K) with an IC50 value of 0.036 μM and identified 3988 compounds from three databases (ChEMBL, PubChem and Drug Bank). Using this screening method, we identified around 15 compounds with XP docking scores greater than −8 kcal/mol. Further, prime MM-GBSA calculations have been performed and found compound SCHEMBL19716714 with the highest binding free energy of −83.31 kcal/mol. Finally, four compounds were identified based on glide energy and ΔG bind scores that have the most binding with DG7, DG19, DG20 bases and Lys1535, His1507, Trp1510, Ser1230, which were required for the target enzyme inhibition. Furthermore, molecular dynamics simulation studies of top ligands validate the stability of the docked complexes by examining root mean square deviations, root mean square fluctuations, solvent accessible surface area, and radius of gyration graphs from simulation trajectories. These findings suggest that the top four hit compounds may be capable of inhibiting DNMT1 and that additional in vitro and in vivo studies will be essential to prove the clinical effectiveness of the selected lead compounds. Communicated by Ramaswamy H. Sarma

Structure-based discovery of novel α-aminoketone derivatives as dual p53-MDM2/MDMX inhibitors for the treatment of cancer

The function of the p53 protein is impaired by the overexpression of its negative regulator murine double minute 2 protein (MDM2) and homologous protein MDMX. Disruption of the p53-MDM2/MDMX interaction to restore the transcriptional function of p53 is considered a promising strategy for cancer therapy. To design dual MDM2/MDMX inhibitors, the binding modes of MDM2 or MDMX with their inhibitors are elucidated. Several hot-spot residues of MDM2 or MDMX are identified by molecular dynamics simulations, alanine scanning and MM-GBSA calculations. Then, focusing on the interaction with hot-spot residues, two series of derivatives bearing 1,3-diketone and α-aminoketone scaffolds are designed and synthesized. Among these compounds, C16 is identified as the most potent compound with low micromolar binding affinities with MDM2 and MDMX. C16 also displays moderate antiproliferative activities against MDM2-overexpressing and MDMX-overexpressing cells, with IC50 values of 0.68 μM in HCT116 cells and 0.54 μM in SH-SY5Y cells. Furthermore, C16 inhibits cell migration and invasion, reactivates the function of p53, arrests the cell cycle and induces cellular apoptosis in HCT116 and SH-SY5Y cells. Collectively, C16 can be developed as a dual MDM2 and MDMX inhibitor for cancer therapy.

Deciphering Selectivity Mechanism of BRD9 and TAF1(2) toward Inhibitors Based on Multiple Short Molecular Dynamics Simulations and MM-GBSA Calculations

BRD9 and TAF1(2) have been regarded as significant targets of drug design for clinically treating acute myeloid leukemia, malignancies, and inflammatory diseases. In this study, multiple short molecular dynamics simulations combined with the molecular mechanics generalized Born surface area method were employed to investigate the binding selectivity of three ligands, 67B, 67C, and 69G, to BRD9/TAF1(2) with IC50 values of 230/59 nM, 1400/46 nM, and 160/410 nM, respectively. The computed binding free energies from the MM-GBSA method displayed good correlations with that provided by the experimental data. The results indicate that the enthalpic contributions played a critical factor in the selectivity recognition of inhibitors toward BRD9 and TAF1(2), indicating that 67B and 67C could more favorably bind to TAF1(2) than BRD9, while 69G had better selectivity toward BRD9 over TAF1(2). In addition, the residue-based free energy decomposition approach was adopted to calculate the inhibitor-residue interaction spectrum, and the results determined the gatekeeper (Y106 in BRD9 and Y1589 in TAF1(2)) and lipophilic shelf (G43, F44, and F45 in BRD9 and W1526, P1527, and F1528 in TAF1(2)), which could be identified as hotspots for designing efficient selective inhibitors toward BRD9 and TAF1(2). This work is also expected to provide significant theoretical guidance and insightful molecular mechanisms for the rational designs of efficient selective inhibitors targeting BRD9 and TAF1(2).

Imidazole-Based Alkaloids from Marine Sponges (Leucetta and Clathrina) as Potential Inhibitors Targeting SARS-CoV-2 Main Protease: An In Silico Approach

Imidazole-based compounds form a prominent class of heterocyclic compounds, displaying diverse applications, especially with regards to its biological and pharmacological activities. Molecular docking, simulations, and drug-likeness prediction were performed on 45 imidazole-based alkaloids from two species of marine sponges (Leucetta and Clathrina). The study seeks to identify possible inhibitors of the SARS-CoV-2 Main Protease in an effort to battle the prevailing pandemic which has been caused by the widespread infections of the SAR-CoV-2 virus in its varied mutated forms. Computational analysis with MOE 2015.10 program reveals that, among the imidazole-based alkaloids, Naamidines have a high affinity for the target protein (PDB ID:6W63), even interacting with the catalytic dyad, as compared to its non-covalent inhibitor X77. Among all the top-scoring ligands, Naamidine H produced the highest binding score of −8.87078 kcal/mol. MD simulation studies with NAMD confirms the stability of the interactions of Naamidines with the target protein. MM-GBSA calculations were performed on the top binding ligands which further confirms the binding affinity of the top-scoring ligands. Computational and pharmacological investigations in this study proposes Naamidines, as effective inhibitors of Mpro. Naamidine I, Naamidine E, and Pyronaamidine could be potential anti-viral candidates against SAR-CoV-2.

Potential of Prenylated Flavonoid Derivatives from Jackfruit Roots (Artocarpus heterophyllus Lam.) as Liver Anticancer Candidates: In Silico Study

Hepatocellular carcinoma (HCC), or liver cancer, is the fourth largest cancer in Indonesia, with 21,392 new cases and around 20,920 deaths. One of the standard drugs for liver cancer patients is lenvatinib, but lenvatinib has dangerous side effects such as hypertension. Previous studies reported that jackfruit root extract (Artocarpus heterophyllus Lam.) contains prenylated flavonoid compounds known to have anticancer activity. This study aims to find compounds that have the potential to the anticancer liver from jackfruit root by understanding the interaction between prenylated flavonoid derivative compounds against the VEGFR2 receptor (PDB ID: 3WZE) in silico. The methods include toxicity and pharmacokinetic screening, drug scanning, docking, and molecular dynamics simulation. The toxicity, pharmacokinetic, and drug scans of cycloartocarpesin are better than lenvatinib. The docking cycloartocarpesin compound showed ∆G -8.49 kcal/mol and Ki 0.59967 M lower than lenvatinib by forming the same hydrogen bond at residue Glu885. The molecular dynamics simulation of the cycloartocarpesin compound in the MM-GBSA calculation method resulted in a ∆Gtotal of -56.641 kcal/mol. The cycloartocarpesin compound is predicted to be used as a candidate for liver anticancer drugs because it has better stability and affinity than lenvatinib.

COVID-19 Activity of Some 9-Anilinoacridines substituted with Pyrazole against SARS CoV2 Main Protease: An In-silico Approach

COVID-19 is affected in more than 200 countries in the world. In this article, some pyrazole bearing 9-anilinoacridines(1a-z) were designed by in-silico studies for SARS-CoV-2 Mpro inhibitory activity. The docking for 1a-z against SARS-CoV-2 Mpro (5R82.pdb) targeting corona virus using Schrodinger suit. The Glide module is used for docking, qikprop for in-silico ADMET screening and Prime MM-GB/SA to determine binding energy of ligands. From the results, many compounds are significantly binding with SARS-CoV-2 Mpro with high G-score when compared to one of the currently recommended drug for COVID19, Hydroxychloroquine (-5.47). From results, many compounds exhibited similar interactions with SARS-CoV-2 Mpro and the aminoacids between GLN19 and GLY143 plays major role for binding. The in-silico ADMET properties are within the recommended values. The MM-GBSA calculations for most of the potent inhibitors are stable. In conclusion, 1t,m,j,o are SARS-CoV-2 Mpro inhibitors and may be useful for significant COVID19 activity after further refinement.

Exploring quantum computational, molecular docking, and molecular dynamics simulation with MMGBSA studies of ethyl-2-amino-4-methyl thiophene-3-carboxylate

2-aminothiophenes derivative, Ethyl-2-amino-4-methyl thiophene-3-carboxylate (EAMC) has been synthesized, characterized, and investigated quantum chemically. It was experimentally investigated by different spectroscopic methods like- NMR (1H-NMR and 13C-NMR), FT-IR, and UV-Visible. B3LYP method and 6-311++G(d,p) basis set were employed for optimization of molecular structure and calculation of wave numbers of normal modes of vibrations and various other important parameters. Calculated bond lengths and angles were compared with the experimental bond lengths and Bond Angle Parameters. Optimized bond parameters and experimental bond parameters were found in good agreement. Complete potential energy distribution assignments were done successfully by VEDA. The HOMO/LUMO energy gap emphasizes adequate charge transfer happening within the molecule. A study of donor-acceptor interconnections was done via NBO analysis. MEP surface analysis was done to demonstrate charge distribution and reactive areas qualitatively in the molecule. The degree of relative localization of electrons was analyzed via ELF Diagram. The Fukui function analysis showed possible sites for attacks by different substituents. By using the TD-DFT method and PCM solvent model, the UV–Vis spectrum (gas, methanol, DMSO) and the maximum absorption wavelength was computed and compared with experimental data. 3D and 2D intermolecular interactions in the crystal were analyzed via Hirshfeld surface analysis and fingerprint plots reveal that the EAMC crystal was stabilized by H–-H/H–-H/C–-H bond formation. The molecular docking was done with 7 different protein receptors on the molecule to find the best ligand-protein interactions. Molecular dynamic simulations and MMGBSA calculations were also carried out to find out the best binding of the ligand with the protein. Communicated by Ramaswamy H. Sarma

Discovery, synthesis and in silico approach of pyrrolo [3,4-c]pyrroles as SARS-CoV-2 mpro inhibitors

A new coronavirus has been identified as the contributing agent of the severe acute respiratory syndrome (SARS). The main viral protease (Mpro), which controls the activities of the coronavirus replication complex, which is an essential target for the treatment of coronavirus disease. With the primary objective of targeting this receptor, we designed a new series of pyrrolo [3,2-c] pyrroles, synthesized and characterized using various analytical techniques including FT-IR, UV-Vis and NMR spectroscopic studies. The biological descriptors of the synthesized compounds were investigated using DFT calculation. The mode of binding and reactivity of the target compounds with SARS-CoV-2 main protease (Mpro) were studied using molecular docking and molecular dynamics (MD) simulation. Molecular docking of the compounds (4a and 5a) showed a promising binding affinity towards Mpro protein with the binding energy of −7.8 kcal/mol and −7.0 kcal/mol, respectively. The results of MD simulation and prime MM-GBSA calculation were consistent with molecular docking. The absorption, distribution, metabolism and excretion (ADME) properties of the compounds are in the acceptable range, as they are orally active and obey Lipinski’s rule of five without violation. In addition, in silico toxicity prediction using the Pro-Tox II revealed the non-toxic nature of the compounds. Hence the obtained results suggest that these compounds could be a possible anti-viral candidate and highlight this series of compounds for further drug design and development against SARS-CoV-2. Communicated by Ramaswamy H. Sarma

Investigating the potential anticancer activities of antibiotics as topoisomerase II inhibitors and DNA intercalators: in vitro, molecular docking, molecular dynamics, and SAR studies

Topoisomerase II (TOP-2) is a promising molecular target for cancer therapy. Numerous antibiotics could interact with biologically relevant macromolecules and provoke antitumor potential. Herein, molecular docking studies were used to investigate the binding interactions of 138 antibiotics against the human topoisomerase II-DNA complex. Followed by the MD simulations for 200 ns and MM-GBSA calculations. On the other hand, the antitumor activities of the most promising candidates were investigated against three cancer cell lines using doxorubicin (DOX) as a reference drug. Notably, spiramycin (SP) and clarithromycin (CL) showed promising anticancer potentials on the MCF-7 cell line. Moreover, azithromycin (AZ) and CL exhibited good anticancer potentials against the HCT-116 cell line. Finally, the TOP-2 enzyme inhibition assay was carried out to confirm the proposed rationale. Briefly, potent TOP-2 inhibitory potentials were recorded for erythromycin (ER) and roxithromycin (RO). Additionally, a SAR study opened eyes to promising anticancer pharmacophores encountered by these antibiotics. Highlights Molecular docking studies of 139 antibiotics against the topoisomerase II-DNA complex. SP, RO, AZ, CL, and ER were the most promising and commercially available candidates. Molecular dynamics simulations for 200 ns for the most promising five complexes. MM-GBSA calculations for the frontier five complexes. SP and CL showed promising anticancer potentials on the MCF-7 cell line, besides, AZ and CL exhibited good anticancer potentials against the HCT-116 cell line. Potent TOP-2 inhibitory potentials were recorded for ER and RO.

Thiourea derivatives containing 4-arylthiazoles and d-glucose moiety: design, synthesis, antimicrobial activity evaluation, and molecular docking/dynamics simulations.

Some substituted glucose-conjugated thioureas containing 1,3-thiazole ring, 4a-h, were synthesized by the reaction of the corresponding substituted 2-amino-4-phenyl-1,3-thiazoles 2a-h with 2,3,4,6-tetra-O-acetyl-β-d-glucopyranosyl isocyanate. The antibacterial and antifungal activities of these thiazole-containing thioureas were estimated using a minimum inhibitory concentration protocol. Among these compounds, 4c, 4g, and 4h were better inhibitors with MIC = 0.78-3.125 μg mL-1. These three compounds were also tested for their ability to inhibit S. aureus enzymes, including DNA gyrase, DNA topoisomerase IV (Topo IV), and dihydrofolate reductase, and compound 4h was found to be a strong inhibitor with IC50 = 1.25 ± 0.12, 67.28 ± 1.21, and 0.13 ± 0.05 μM, respectively. Induced-fit docking and MM-GBSA calculations were performed to observe the binding efficiencies and steric interactions of these compounds. The obtained results showed that compound 4h is compatible with the active site of S. aureus DNA gyrase 2XCS with four H-bond interactions with residues Ala1118, Met1121, and F:DC11 and also three interactions with F:DG10 (two interactions) and F:DC11 (one interaction). Molecular dynamics simulation in a water solvent system showed that ligand 4h had active interactions with enzyme 2XCS through residues Ala1083, Glu1088, Ala1118, Gly1117, and Met1121.

Discovery of Pongol, the Furanoflavonoid, as an Inhibitor of CDK7/Cyclin H/MAT1 and Its Preliminary Structure-Activity Relationship.

Natural products have been a great source of leads for cancer drug discovery. The cyclin-dependent kinases (CDKs) play a vital role in the initiation and progression of cancer. The CDK-activating kinase, CDK7/cyclin H/MAT1, has recently gained tremendous attention in targeted cancer drug discovery. Herein, we screened a small library of pure natural products in an ADP-Glo CDK7/H kinase assay that yielded a series of furano- and naphthoflavonoids among actives. Pongol (SBN-88), the hydroxy-substituted furanoflavonoid, inhibits CDK7/H as well as CDK9/T1 with IC50 values of 0.93 and 0.83 μM, respectively, and >20-fold selectivity over CDK2/E1 (IC50 > 20 μM). The molecular docking and molecular dynamics simulation revealed that the presence of phenolic -OH in pongol is vital for kinase inhibition, as its absence resulted in a significant loss in activity (e.g., lanceolatin B). The prime MM-GBSA calculations revealed the presence of strong lipophilic and H-bonding interactions of pongol with CDKs.

Bioactive compounds from Pandanous fascicularis as potential therapeutic candidate to tackle hepatitis a inhibition: Docking and molecular dynamics simulation study

Due to extensive pharmacological research, medicinal plants the underpinning of indigenous herbal serve as a possible source of key compounds for the development of new drugs. Hepatitis A, one of the most widespread infectious diseases associated with global public health issues. The transmission of hepatitis A virus (HAV) occurs, through personal contact, as well as contaminated food/water. The HAV 3C cysteine protease is a non-structural protein, plays pivotal role in proliferation and viral replication. Significant phytochemicals of Pandanous fascicularis include phytosterol, kobusin, epipinoresinol, and ceroptene, which have a wide variety of biological functions. Through ADMET investigation, we have screened fifteen phytochemicals for this study. Additionally, using molecular docking, these phytochemicals were docked with the HAV 3C protease which signifies the phytochemicals phytosterol, kobusin, epipinoresinol, and ceroptene have a significant capability to bind with hepatitis A virus protein.The docking study was further accompanied by analyzes RMSD, RMSF, Rg, SASA, H-bond number, and principal component analysis through 100 ns MD simulations. The molecular dynamics study reveals that, all four phytochemicals possess considerable binding efficacy with hepatitis A virus protein. Based on our computational study and MMGBSA calculations, phytosterol, kobusin and epipinoresinol phytochemicals may be a potential drug candidate for inhibition of hepatitis A. The potential therapeutic characteristics of the phytochemicals against hepatitis A inhibition offer additional support for the in vitro and in vivo studies in future. Communicated by Ramaswamy H. Sarma

Insights from computational studies on the potential of natural compounds as inhibitors against SARS-CoV-2 spike omicron variant

ABSTRACT Coronavirus disease 2019 (COVID-19) is a major global health emergency, with more than six million deaths worldwide. It is becoming increasingly challenging to treat COVID-19 due to the emergence of novel variants. The omicron variant is capable to evade defences and spread quickly. Among many validated COVID-19 targets, the spike (S) protein plays an important role in receptor recognition (via the S1 subunit) and membrane fusion (via the S2 subunit). The S protein is one of the vital targets for the development of drugs to combat this illness. In this research, we applied various computational methods such as molecular docking, molecular dynamics, MM-GBSA calculations, and ADMET prediction to identify potential natural products from Saudi medicinal plants against the spike omicron variant. As a result, three compounds (LTS0002490, LTS0117007, and LTS0217912) were identified with better binding affinity to the spike omicron variant compared to the reference compound (VE607). In addition, these compounds showed stable interactions with the target during molecular dynamics simulations for 140 ns. Last, these compounds have optimal ADMET properties. We suggest that these compounds may be considered promising hits to treat COVID-19 if experimentally validated.

Insight into the conformational analysis of 3-phenyl-N-(3-(trimethoxysilyl) propyl)prop-2-en-1-imine (PTP) as a biocidal candidate: In-silico and quantum computational approach

A newly synthesized compound, 3-phenyl-N-(3-(trimethoxysilyl) propyl)prop-2-en-1-imine (PTP) is analyzed in detail for structural clarification by mass spectroscopy & FT-IR along with theoretical quantum chemical computations. The conformers of the structure were optimized through DFT to understand the stable conformer (1Z2E) of the structure and their interaction with the protein. The docking studies of the synthesized compound were carried out to determine the interaction with the receptor protein Dihydropteroate synthase protein (PDB ID: 3TZF) which showed very good interactions with various amino acid residues like HIS203, LEU194, LEU40, and so on. Molecular dynamic simulation of the title compound was made to understand the stability of the docked complex. The MM-GBSA calculations verify that the stable conformer (1Z2E) efficiently binds to selected protein to form a stable protein–ligand complex. The in-silico results revealed that in the future PTP can be used for further development, to treat the antibacterial infection.

Structural, Quantum Chemical, Molecular Docking, and Dynamics Studies of Quercetin—A Potent Inhibitor for Colon Cancer

According to several studies, phytochemicals, such as polyphenols, flavones, and flavonoids have significant anticancer properties that can combat various malignancies. Even though its action is highly dependent on the intracellular availability of reduced glutathione, Quercetin is regarded as an excellent free-radical scavenging antioxidant flavonoid. Apart from its antioxidant properties, Quercetin has a direct pro-apoptotic action in tumor cells. It has been shown to inhibit the proliferation of multiple human cancer cell lines at various cell cycle stages. The choice of a suitable chemopreventive agent was based on epidemiological studies that showed that consuming a specific dietary component (e.g. Quercetin) can lower the incidence of specific cancer death. MLK4 (KIAA1804) is the second most often altered kinase in colorectal carcinomas with microsatellite stability (MSS) (CRC). MLK4 regulates various physiological cellular processes, including cell cycle, senescence, and apoptosis, and mechanistic evidence suggests MLK4 is involved in carcinogenesis. In this study, the molecular structure of the Quercetin molecule was optimized using DFT/B3LYP method with a cc-pVTZ basis set, and the structural parameters were calculated. The generated vibrational spectra and the optimized molecular geometry were thoroughly reviewed and compared with experimental findings, resulting in a strong correlation. FMOs analysis was performed, which confirms the molecular reactivity of the Quercetin molecule. The anti-tumor efficacy of Quercetin was examined against the colon cancer target protein through in silico parameters, such as molecular docking and dynamics, ADME studies, MM-GBSA calculations, and the Pharmacophore hypothesis. From the analysis, the docked complex showed the highest docking score and maintained the complex stability and flexibility throughout the simulation period. Thus, the present study concluded that Quercetin could be a potent inhibitor of targeted colon cancer protein.

Selectivity mechanism of GRK2/5 inhibition through in silico investigation

As two representative isoforms of G protein-coupled receptor kinases family, the largest known membrane receptor family, GRK2 and GRK5 are ubiquitously distributed in human heart, brain, lung, kidney, skeletal muscle and other tissues. GRK2 and GRK5 have common functions implicated in the regulation of heart failure, though GRK5 has also been involved in diseases like hypertension, cancer, diabetes and Alzheimer's disease. Therefore, to clarify the selectivity mechanism towards GRK2 and GRK5 will be of great significance for the discovery of effective and selective inhibitors. To this end, the structures and chemical properties of key residues were analyzed among GRK2 and GRK5 derived from their respective protein crystal structures. Furthermore, a combination of multiple computational strategies, including sequence superposition, receptor-ligand docking, molecular dynamics, MM-GBSA calculation, QM/MM approach and pharmacological modeling, were integrated to validated and elucidate their unique binding modes towards highly selective inhibitors. In addition, the specific amino acid distribution within the GRK2/5 target site is also analyzed in this paper, which can guide future research and development of selective inhibitors in a more targeted manner. Overall, our study comprehensively clarifies the selectivity mechanism of GRK2/5 inhibition, thereby providing guidance for further rational design of selective inhibitors targeting GRK2/5.

Theoretical studies, spectroscopic investigation, molecular docking, molecular dynamics and MMGBSA calculations with 2‐hydrazinoquinoline

We report a comprehensive account on the theoretical and spectroscopic study of 2-hydrazinoquinoline. Computational studies have been performed using density functional theory (DFT) via B3LYP functional and 6-311++G (d,p) basis set. The theoretically predicted spectra showed good agreement with the experimentally obtained IR, NMR and UV spectra. TD-DFT provided information regarding the electronic transition probabilities. Calculation of the energy and structures of the FMO helped in understanding the stability, reactivity and other vital molecular properties. The NBO analysis afforded the insights on the various donor–acceptor interactions at the orbital level, that are responsible for stabilizing the molecule. The distribution of electron density across the molecule was studied using molecular electrostatic potential (MEP). The ELF studies were used to identify the electronic localization within the molecule. The pharmaco-kinetic properties along with the drug-likeness was analyzed as a part of understanding the therapeutic potential of the molecule. Molecular docking studies with four macromolecular targets (COVID-19 viral main protease, FABG4 enzyme, Cruzain and RIP2 Kinase) revealed reasonably good binding affinities. The stability of the best two docked-complexes were investigated using 200ns molecular dynamics simulation followed by effective free energy calculation using MMGBSA.

Discovery of Novel and Potent Inhibitors Against Mutational Variants of IDH1 Protein for Glioma Therapy: A Fragment-Based Approach

Somatic mutations in the isoenzymes of isocitrate dehydrogenases (IDHs) account for the pathogenesis of various malignancies including gliomas. To date, ivosidenib is the only FDA-approved drug candidate widely used to target mutated isocitrate dehydrogenase 1 (mIDH1). However, the impotence of the existing drug to evade the blood barrier remains an obstacle to harness ivosidenib as therapeutics against glioma. Thus, in this study, we elucidate a fragment-based drug discovery strategy to design novel lead molecules against the mIDH1 protein. Initially, a fragment library was constructed using 27 known mIDH1 inhibitors from the literature. The vast chemical classes of constructed library consisting of 1109 fragments were then used for breeding. A total of 18,000 breed compounds were generated and the resultant compounds were scrutinized based on the breed score ([Formula: see text]) and Tanimoto coefficient ([Formula: see text]). The binding affinity and the energetics of the resultant molecules (2069) were investigated using molecular docking and MM-GBSA calculations. Eventually, the compounds with higher affinity were included in the mutational analysis incorporating the second site mutations namely IDH1S280F and IDH1R119P. The bioavailability analysis and toxicity profiling were carried out for screened hybrid molecules. The pipeline of the integrated in-silico approach identified hybrid 209, hybrid 237 and hybrid 504 as the drug-like candidates against the mutational variants of mIDH1 protein. Interestingly, all three compounds exhibited greater binding affinity and better brain penetrating capability. The machine learning-based anti-cancerous sensitivity prediction tool affirmed the inhibitory effect of the resultant hits against various glioma cell lines. In the end, the structural stability of the screened molecules was examined using the molecular dynamic simulation study for a stipulated time of 100[Formula: see text]ns. Indeed, this evidence speculates that the identified hybrid molecules could serve as important leads for the management of glioma in the near future.

Identification of 1H-purine-2,6-dione derivative as a potential SARS-CoV-2 main protease inhibitor: molecular docking, dynamic simulations, and energy calculations.

The rapid spread of the coronavirus since its first appearance in 2019 has taken the world by surprise, challenging the global economy, and putting pressure on healthcare systems across the world. The introduction of preventive vaccines only managed to slow the rising death rates worldwide, illuminating the pressing need for developing effective antiviral therapeutics. The traditional route of drug discovery has been known to require years which the world does not currently have. In silico approaches in drug design have shown promising results over the last decade, helping to decrease the required time for drug development. One of the vital non-structural proteins that are essential to viral replication and transcription is the SARS-CoV-2 main protease (Mpro). Herein, using a test set of recently identified COVID-19 inhibitors, a pharmacophore was developed to screen 20 million drug-like compounds obtained from a freely accessible Zinc database. The generated hits were ranked using a structure based virtual screening technique (SBVS), and the top hits were subjected to in-depth molecular docking studies and MM-GBSA calculations over SARS-COV-2 Mpro. Finally, the most promising hit, compound (1), and the potent standard (III) were subjected to 100 ns molecular dynamics (MD) simulations and in silico ADME study. The result of the MD analysis as well as the in silico pharmacokinetic study reveal compound 1 to be a promising SARS-Cov-2 MPro inhibitor suitable for further development.

Abetting host immune response by inhibiting rhipicephalus sanguineus Evasin-1: An in silico approach.

The brown dog tick (Rhipicephalus sanguineus) is the most prevalent tick in the world and a well-recognized vector of many pathogens affecting dogs and occasionally humans. Pathogens exploit tick salivary molecules for their survival and multiplication in the vector and transmission to and establishment in the hosts. Tick saliva contains various non-proteinaceous substances and secreted proteins that are differentially produced during feeding and comprise of inhibitors of blood congealing and platelet aggregation, vasodilatory and immunomodulatory substances, and compounds preventing itch and pain. One of these proteins is Evasin-1, which has a high binding affinity to certain types of chemokines. The binding of Evasin-1 to chemokines prevents the detection and immune response of the host to R. sanguineus, which may result in the successful transmission of pathogens. In this study, we screened potential Evasin-1 inhibitor based on the pharmacophore model derived from the binding site residues. Hit ligands were further screened via molecular docking and virtual ADMET prediction, which resulted in ZINC8856727 as the top ligand (binding affinity: -9.1 kcal/mol). Molecular dynamics simulation studies, coupled with MM-GBSA calculations and principal component analysis revealed that ZINC8856727 plays a vital role in the stability of Evasin-1. We recommend continuing the study by developing a formulation that serves as a potential medicine aid immune response during R. sanguineus infestation.