Co-crystal Ligand Research Articles

Coumarin-based C-2 cycloalkylated histidine derivatives: Design, synthesis, biological evaluation, molecular docking and MD simulation studies as potential antimicrobial agents

Despite numerous attempts to develop new pharmacophores as promising antimicrobials, the coumarin scaffold remains one of the foremost sought moiety in the design of molecules. Herein, we report the new structural class of coumarin-based C-2 cycloalkylated histidine hybrids as potential antimicrobial agents. The most promising compound 11n displayed IC50 of 0.27 µg/mL, 1.1 µg/mL, 4.4 µg/mL and 4.4 µg/mL against Crptococcus neoformans, Candida albicans, Escherichia coli and Staphylococcus aureus, respectively. Interestingly, 11n displays fungicidal activity on growing cryptococcal cells with high selectivity. The presence of 11n lead to the permeabilization of fungal cells as confirmed by propidium iodide uptake study. Moreover, scanning electron microscopy revealed that it causes shrinkage and disruptions in the cell membranes, which is responsible for the cell lysis. Molecular docking analysis revealed that 11n have a distinct H-bonding with TYR409 and TRP94 which are lacking in the co-crystal ligand and are predicted that these are responsible for the potency of the compound. Moreover, the results of the MD simulation analysis showed that the protein-ligand complex exhibits substantial binding interactions with a variety of amino acids and is stable for 100 ns. Additionally, ADMET analysis depicted that these molecules have considerable ADME properties.

Identification of novel scaffolds targeting SIRT3 through molecular modeling techniques for the treatment of Hepatocellular carcinoma

Hepatocellular carcinoma is one of the top causes of cancer-related death globally. SIRT3 belongs to the Sirtuin family of proteins, a collection of NAD+-dependent enzymes that play a role in controlling several cellular functions, including metabolism, aging, and stress response. SIRT3 expression has been discovered to be often downregulated in HCC tissues relative to normal liver tissues. Hence, SIRT3 may function as a tumor suppressor in HCC. In the present study, pharmacophore-based virtual screening of a small molecule database was performed initially, and then the screened hits were docked to the active site of SIRT3 to choose the best binding modes. One co-crystal ligand (PDB name: 1NQ) was utilized as a template to generate pharmacophore model query. A total of 0.2 million compounds from the VITAS-M Lab database were downloaded and prepared for virtual screening. Following database preparation, ligand-based virtual screening was performed using the pharmacophore query model generated in the previous phase. The compounds with the same pharmacophoric characteristics as the query at the same distance were screened. There were a total of 74 hits that matched the query model. These compounds were then docked to the SIRT3 using the standard precision protocol of the glide tool. To select hits with high binding affinities, a threshold of −8 kcal/mol was used. Based on the glide gscore, two hits were chosen. These two hits were selected to investigate the stability of the protein-ligand complex by molecular dynamics simulation. All of these findings indicate that the selected hit compounds C1 and C2 can serve as lead compounds in inhibiting the biological activity of SIRT3 requiring further detailed investigations. Communicated by Ramaswamy H. Sarma

IN SILICO EVALUATION OF SARS-COV-2 PAPAIN-LIKE PROTEASE INHIBITORY ACTIVITY OF SOME FDA-APPROVED DRUGS

Objective: In this study, it was aimed to perform in silico studies on the papain-like protease structure of SARS-CoV-2 (PDB: 7JIT) of 1300 FDA-approved drugs downloaded from the ZINC database. Material and Method: A molecular docking study was performed with PLpro (PDB ID: 7JIT) using four different molecular docking programs for a total of 1300 FDA-approved drugs obtained from the ZINC database. Conivaptan and amphotericin B were obtained in docking analysis with AutoDock Vina and Sybyl-X, respectively. Docking analysis with Glide SP and Glide XP resulted in fludarabine and panobinostat, respectively. Molecular dynamics simulations were performed for a period of 120 ns to check the stability of these four drugs. Result and Discussion: The reliability of the results obtained using four different molecular docking programs on the SARS-CoV-2 papain-like protease of 1300 drug molecules was checked by reinserting the co-crystal ligand. Protein-ligand interactions between fludarabine, conivaptan, amphotericin-B, panobinostat, and PLpro were given. In the molecular dynamics study, RMSD, RMSF, Rg, and SASA analyses were performed for four systems. It was observed that RMSD remained constant for all 120 ns for all four systems except for amphotericin B, which deviated slightly towards the end of 120 ns. No significant fluctuation was noticed in the RMSF graphics for all four systems.

A systematic pipeline of protein structure selection for computer-aided drug discovery: A case study on T790M/L858R mutant EGFR structures.

Virtual screening (VS) is a routine method to evaluate chemical libraries for lead identification. Therefore, the selection of appropriate protein structures for VS is an essential prerequisite to identify true actives during docking. But the presence of several crystal structures of the same protein makes it difficult to select one or few structures rationally for screening. Therefore, a computational prioritization protocol has been developed for shortlisting crystal structures that identify true active molecules with better efficiency. As identification of small-molecule inhibitors is an important clinical requirement for the T790M/L858R (TMLR) EGFR mutant, it has been selected as a case study. The approach involves cross-docking of 21 co-crystal ligands with all the structures of the same protein to select structures that dock non-native ligands with lower RMSD. The cross docking performance was then correlated with ligand similarity and binding-site conformational similarity. Eventually, structures were shortlisted by integrating cross-docking performance, and ligand and binding-site similarity. Thereafter, binding pose metadynamics was employed to identify structures having stable co-crystal ligands in their respective binding pockets. Finally, different enrichment metrics like BEDROC, RIE, AUAC, and EF1% were evaluated leading to the identification of five TMLR structures (5HCX, 5CAN, 5CAP, 5CAS, and 5CAO). These structures docked a number of non-native ligands with low RMSD, contain structurally dissimilar ligands, have conformationally dissimilar binding sites, harbor stable co-crystal ligands, and also identify true actives early. The present approach can be implemented for shortlisting protein targets of any other important therapeutic kinases.

Phenolic compounds as potential adenosine deaminase inhibitors: molecular docking and dynamics simulation coupled with MM-GBSA calculations.

Adenosine deaminase (ADA) is a Zn2+-containing enzyme that catalyzes the irreversible deamination of adenosine to inosine or deoxyadenosine to deoxyinosine. In addition to this enzymatic function, ADA mediates cell-to-cell interactions involved in lymphocyte co-stimulation or endothelial activation. ADA is implicated in cardiovascular pathologies such as atherosclerosis and certain types of cancers, including lymphoma and leukemia. To date, only two drugs (pentostatin and cladribine) have been approved for the treatment of hairy cell leukemia. In search of natural ADA inhibitors, we demonstrated the binding of selected phenolic compounds to the active site of ADA using molecular docking and molecular dynamics simulation. Our results show that phenolic compounds (chlorogenic acid, quercetin, and hyperoside) stabilized the ADA complex by forming persistent interactions with the catalytically essential Zn2+ ion. Furthermore, MM-GBSA ligand binding affinity calculations revealed that hyperoside had a comparable binding energy score (ΔG = -46.56 ± 8.26kcal/mol) to that of the cocrystal ligand in the ADA crystal structure (PDB ID: 1O5R) (ΔG = -51.97 ± 4.70kcal/mol). Similarly, chlorogenic acid exhibited a binding energy score (ΔG = -18.76 ± 4.60kcal/mol) comparable to those of the two approved ADA inhibitor drugs pentostatin (ΔG = -14.54 ± 2.25kcal/mol) and cladribine (ΔG = - 25.52 ± 4.10kcal/mol) while quercetin was found to have modest binding affinity (ΔG = - 8.85 ± 7.32kcal/mol). This study provides insights into the possible inhibitory potential of these phenolic compounds against ADA.

Discovery of a new Daboia russelli viper venom PLA2 inhibitor using virtual screening of pharmacophoric features of co-crystallized compound

Snake venom PLA2, a member of the group of hydrolase enzymes, has been recognized as a promising drug target for snake envenomation. In the present study, an attempt was made to identify potential inhibitors of snake venom PLA2 by employing a pharmacophore-based virtual screening, docking, and dynamics approach. A receptor-based pharmacophore model was generated based on the features of the established and bound co-crystal ligand (2-carbamoylmethyl-5-propyl-octahydro-indol-7-yl)-acetic acid in the PLA2 complex. The best pharmacophore model (ADDH) derived, consisted of four features, namely one hydrogen bond acceptor, two hydrogen bond donors, and one hydrophobic region. This common pharmacophore was then used to perform virtual screening against a drug-like diverse database, with due consideration to the Lipinski ‘rule of five’, so as to obtain a pool of lead molecules. The short-listed lead molecules were then subjected to docking analysis with that of the Daboia russelli viper venom PLA2 followed by a molecular simulation study for a duration of 100 ns. CAP04815700 was chosen as the best compound based on the simulation parameters, which were then taken for MM/PBSA calculation, and it was revealed that it has a similar effective inhibitory potential as that of the crystal ligand. Further, the cluster analysis also revealed the structural significance of the backbone protein after the interaction with CAP04815700. This study will continue to explore its bioactivity in vitro and in vivo. Communicated by Ramaswamy H. Sarma

Design, synthesis, and biological studies of novel sulfonamide derivatives as farnesoid X receptor agonists

Farnesoid X receptor (FXR) is considered as a promising target for the treatment of NASH. Although many non-steroidal FXR agonists have been reported, the structure types are quite scarce and mainly limited to the isoxazole scaffold derived from GW4064. Therefore, it is crucial to expand the structure types of FXR agonist to explore wider chemical space. In this study, the structure-based scaffold hopping strategy was performed by hybrid FXR agonist 1 and T0901317, which resulted in the discovery of sulfonamide FXR agonist 19. Molecular docking study reasonably explained the SAR in this series, and compound 19 fitted well with the binding pocket in a similar mode to the co-crystal ligand. In addition, compound 19 exhibited considerable selectivity against other nuclear receptors. In NASH model, compound 19 alleviated the typical histological features of fatty liver, including steatosis, lobular inflammation, ballooning, and fibrosis. Moreover, compound 19 exhibited acceptable safety profiles with no acute toxicity to major organ. These results suggested that the novel sulfonamide FXR agonist 19 might be a promising agent for the treatment of NASH.

Potential mechanisms of osthole against bladder cancer cells based on network pharmacology, molecular docking, and experimental validation

BackgroundOsthole was traditionally used in treatment for various diseases. However, few studies had demonstrated that osthole could suppress bladder cancer cells and its mechanism was unclear. Therefore, we performed a research to explore the potential mechanism for osthole against bladder cancer.MethodsInternet web servers SwissTargetPrediction, PharmMapper, SuperPRED, and TargetNet were used to predict the Osthole targets. GeneCards and the OMIM database were used to indicate bladder cancer targets. The intersection of two target gene fragments was used to obtain the key target genes. Protein–protein interaction (PPI) analysis was performed using the Search Tool for the Retrieval of Interacting Genes (STRING) database. Furthermore, we used gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses to explore the molecular function of target genes. AutoDock software was then used to perform molecular docking of target genes,osthole and co-crystal ligand. Finally, an in vitro experiment was conducted to validate bladder cancer inhibition by osthole.ResultsOur analysis identified 369 intersection genes for osthole, the top ten target genes included MAPK1, AKT1, SRC, HRAS, HASP90AA1, PIK3R1, PTPN11, MAPK14, CREBBP, and RXRA. The GO and KEGG pathway enrichment results revealed that the PI3K-AKT pathway was closely correlated with osthole against bladder cancer. The osthole had cytotoxic effect on bladder cancer cells according to the cytotoxic assay. Additionally, osthole blocked the bladder cancer epithelial-mesenchymal transition and promoted bladder cancer cell apoptosis by inhibiting the PI3K-AKT and Janus kinase/signal transducer and activator of transcription (JAK/STAT3) pathways.ConclusionsWe found that osthole had cytotoxic effect on bladder cancer cells and inhibited invasion, migration, and epithelial-mesenchymal transition by inhibiting PI3K-AKT and JAK/STAT3 pathways in in vitro experiment. Above all, osthole might have potential significance in treatment of bladder cancer.SubjectsBioinformatics, Computational Biology, Molecular Biology.

Exploiting the co-crystal ligands shape, features and structure-based approaches for identification of SARS-CoV-2 Mpro inhibitors

SARS-CoV-2 enters the host cell through the ACE2 receptor and replicates its genome using an RNA-Dependent RNA Polymerase (RDRP). The functional RDRP is released from pro-protein pp1ab by the proteolytic activity of Main protease (Mpro) which is encoded within the viral genome. Due to its vital role in proteolysis of viral polyprotein chains, it has become an attractive potential drug target. We employed a hierarchical virtual screening approach to identify small synthetic protease inhibitors. Statistically optimized molecular shape and color-based features (various functional groups) from co-crystal ligands were used to screen different databases through various scoring schemes. Then, the electrostatic complementarity of screened compounds was matched with the most active molecule to further reduce the hit molecules’ size. Finally, five hundred eighty-seven molecules were docked in Mpro catalytic binding site, out of which 29 common best hits were selected based on Glide and FRED scores. Five best-fitting compounds in complex with Mpro were subjected to MD simulations to analyze their structural stability and binding affinities with Mpro using MM/GB(PB)SA models. Modeling results suggest that identified hits can act as the lead compounds for designing better active Mpro inhibitors to enhance the chemical space to combat COVID-19.Communicated by Ramaswamy H. Sarma

Phenolic compounds as histone deacetylase inhibitors: binding propensity and interaction insights from molecular docking and dynamics simulations.

Histone deacetylases are well-established target enzymes involved in the pathology of different diseases including cancer and neurodegenerative disorders. The approved HDAC inhibitor drugs are associated with cellular toxicities. Different phenolic compounds have been shown to possess inhibitory activities against HDACs and are, therefore, considered safer alternatives to synthetic compounds. Here, we elucidated the binding mode and calculated the binding propensity of some of the top phenolic compounds against different isoforms representing different classes of Zn2+ ion-containing HDACs using the molecular docking approach. Our data reaffirmed the activity of the studied phenolic compounds against HDACs. Binding interaction analysis suggested that these compounds can block the activity of HDACs with or without binding to the active site zinc metal ion. Furthermore, molecular dynamics (MD) simulations were carried out on the selected crystal and docking complexes of each selected HDAC isoform. Analysis of root-mean-square displacement (RMSD) showed that the phenolic compounds demonstrated a stable binding mode over 50ns in a way that is comparable to the cocrystal ligands. Together, these findings can aid future efforts in the search for natural inhibitors of HDACs.

Green Route Synthesis and Molecular Docking of Azines Using Cellulose Sulfuric Acid under Microwave Irradiation

A novel catalytic approach for the synthesis of symmetric and asymmetric azines has been developed. The environmentally benign protocol was achieved via condensation of 1-[(2-thienyl)ethylidene]hydrazine (1) with different aromatic aldehydes 2a–h and acetyl heterocyclic compounds (4, 6, 8, 10, and 12) in the presence of cellulose sulfuric acid (CSA) as the green catalyst. These procedures offer an interesting method for the large-scale industrial manufacture of azines due to their high percentage yield, mild reaction conditions, broad substrate range, and utilization of an economical and environmentally acceptable catalyst. Additionally, the molecular docking of the products to the monoamine oxidase (MAO-A) target protein was achieved to highlight the possible binding interaction with the amino acid residues Arg51, Glu43, Gly22, Gly49, Gly443, Ala272, Ile335, and Tyr407 at the point of binding. The binding interaction energy was discovered to be (− 6.48 kcal/mol) for the protein MAO-A (PDB ID: 2Z5X). The most effective azine derivatives 7 and 13 revealed some major conserved interactions between the MAO-A protein’s binding site amino acid residues and the PDB co-crystal ligand 2Z5X. Moreover, azine derivatives 3a and 3f showed the lowest binding activity with the target MAO-A.

Insights from the molecular docking analysis of GRP78 with natural compound inhibitors in the management of cancers.

Cancer is regarded as one of the world's most serious health issues. Glucose regulated protein (GRP78) exhibits a vital role in the proliferation, invasion, and metastasis of numerous cancer cells. Based on that, this study screened the 390 natural compounds targeting the GRP78 catalytic site. Among them, corynanthin, toyocamycin, and nanaomycin were found to strongly bind with GRP78 and possess the binding affinities of -8.4, -8.9, and -8.7 kcal/mol, respectively. In addition, these compounds interacted with key residues of GRP78 and have several amino acid residues interaction in common with the cocrystal ligand (ATP). Based on physicochemical parameters and ADME evaluations, these compounds were found to have good drug-like properties. These compounds could be used as possible GRP78 inhibitors in the fight against cancers. Albeit, exhaustive experimental studies would be required to confirm the findings described here.

AN In-silico MOLECULAR DOCKING STUDY ON THE INTERACTION OF DIFFERENT PARABEN ESTERS (METHYL-, ETHYL-, PROPYL- AND BUTYL-PARABEN) WITH HUMAN THYROID HORMONE RECEPTOR α1 (THRα1) AND β1 (THRβ1)

Thyroid hormones (THs) activate transcription of a large number of genes via binding with nuclear thyroid hormone receptors (THRs) that are either attached to the DNA genetic strands or located in proximity to them. However, the ever-increasing human anthropogenic activities have introduced numerous harmful chemicals in the environment, many of which share high degree of structural resemblance with the THs i.e., triiodothyronine (T3) and thyroxine (T4) and thus can interfere with the normal downstream receptor signalling. The present study used bioinformatics to perform a molecular docking analysis (Autodock 4.2.6) where different paraben esters (PBs) i.e., methyl- (MP), ethyl- (EP), propyl- (PP) and butyl- paraben (BP) were examined for their possible interaction with two human THR isoforms viz., THRα1 and THRβ1. Perceiving the free binding energies (ΔG) of different PB-THRs complexes, it has become evident that BP has the strongest binding interaction with both THRα1 (PDB Id- 1NAV) and THRβ1 (PDB Id- 1NAX) i.e., -6.51 and -6.14 kcal/mol respectively and also has highest number of amino acids interactions in the active sites, followed by PP, EP and MP. The co-crystal ligand exhibited binding energies of -10.43 and -10.52 kcal/mol for THRα1 and THRβ1 respectively. Therefore, the study firmly demonstrates that thyroid hormone receptor interaction of the selected PB esters rise with increase in length/complexity of the alkyl side chain. Given that all the investigated PB esters are capable binders of both the THRs, unremitting use of these chemical preservatives certainly could amend the receptor mediated signalling of THs.

Potential Anti-osteoporosis compounds from Zingiber officinale: A Molecular Docking and Pharmacokinetics Prediction

Osteoporosis is a systemic skeletal disease characterized by low bone mass, that can result in fracture when injury, for example, due to a traffic accident. This study aimed to identify secondary metabolites from Zingiber officinale that potentially inhibit cathepsin K, a critical enzyme that caused osteoporosis. In this study, a molecular docking of 102 bioactive compounds from Zingiber officinale against cathepsin K (PDB ID: 4X6I) was conducted. Ligand preparation was performed using JChem and Schrödinger’s software, and virtual protein was elucidated using AutoDockTools version 1.5.6. Cocrystal ligand was carried out as a positive control ligand. Pharmacokinetics of the compounds was predicted with SwissADME online tool. Based on the results, nine compounds had good binding affinity against cathepsin K. The compounds were shogasulfonic acid C, (-)-beta-sitosterol, shogasulfonic acid D, shogasulfonic acid B, shogasulfonic acid A, isogingerenone B, (S)-8-gingerol, gingerenone A, and hexahydrocurcumin, with binding affinities of -7.2, -7.0, -6.9, -6.8, -6.8, -6.7, -6.7, -6.6, and -6.4 kcal mol−1, respectively. Most compounds had great pharmacokinetic profiles and also drug-likeness properties. In conclusion, bioactive compounds from Zingiber officinale are potentially used as anti-osteoporosis agents targeting cathepsin K. However, in vitro and in vivo studies are needed to prove the anti-osteoporosis activity of these compounds.

Design, synthesis and molecular docking study of thiophenyl hydrazone derivatives as tubulin polymerization inhibitors

A series of thiophene derivatives substituted at 2, 3 and 5 positions were designed and synthesized using 2,3-disubstituted thiophene aldehyde and alcohol as key building blocks. Invitro cytotoxicity assessed against PC-3, DU145 (prostate), A549 (lung), HT29, HCT116 (colon), MCF7, MDAMB231 (breast), B16F10 (melanoma) NCI (Colorectal) cancer cell lines by conducting (MTT) assay of thiophene derivatives. Most of these synthesized compounds showed anti-cancer activity, compound 5b showed good cytotoxicity with IC50 = 2.61 ± 0.34 µM on HT29 cell line. Also, the key property of cell migration was observed while treating cells with 5b. The Cell cycle arrest at G2/M phase was observed by 5b on HT29 cell line which inhibited tubulin polymerization with IC50 value of 8.21 ± 0.30 μM. Moreover, binding pose with co-crystal ligand and interaction with colchicine binding site of 5b was established by molecular docking studies. Hence this scaffold can be developed as anti-cancer agents that target tubulin polymerization.

Studies on New Imidazo[2,1-b][1,3,4]thiadiazole Derivatives: Molecular Structure, Quantum Chemical Computational, and In silico Study of Inhibitory Activity Against Pim-1 Protein by using Molecular Modelling Methods and ADMET Profiling

Imidazothiadiazole derivatives (KITD4 and KITD10) have been synthesized and characterized by NMR (1H&13C) spectra and single-crystal X-ray diffraction techniques. Density functional theory (DFT) calculations were performed to investigate the effect of substituents on the structures and intramolecular charge transfer (ICT) using natural bond orbital (NBO) analysis. Furthermore, DFT studies were extended to investigate the reactive sites of the title compounds through the molecular electrostatic potential (MEP) and frontier molecular orbitals (FMOs), including HOMO-LUMO, energy gap, and other chemical reactivity parameters. Hirshfeld surface and energy frameworks evaluated the different intermolecular interactions and energies based on the anisotropy of the topology. SwissADME drug design server predicted the oral bioavailability in the physicochemical space and showed good pharmacokinetic properties based on the boiled egg model. In addition, in silico molecular docking studies were executed to predict the biological activity of the molecules, as anticancer, against Pim-1 protein (homo sapiens PDB id: 3A99) and revealed prominent interactions with the active site of both the ligands showing reasonable conformity with the reported cocrystal ligand interactions. Besides, molecular dynamics simulations of holoprotein confirmed the structural constancy and stability of the protein-ligand complexes with minimal deviation showing faithful convergence throughout the entire trajectory of simulations. Both the simulations justify the hydrogen bond formations of the compounds with the vital amino acid LYS67, which is very much crucial for the inhibition of Pim-1 protein and shows similar conformity of hydrophobic residues interactions.

A computational evaluation of FDA medicines' ability to inhibit hypoxia-inducible factor prolyl hydroxylase-2 (PHD-2) for acute respiratory distress syndrome.

COVID-19 infection is associated with a significant fatality rate in individuals suffering from severe acute respiratory distress syndrome (ARDS). Among the several possibilities, inhibition of hypoxia-inducible factor prolyl hydroxylase-2 or prolyl hydroxylase domain-containing protein 2 (PHD2) in a hypoxia-independent way is a prospective therapeutic target for the treatment of ARDS. Vadadustat, Roxadustat, Daprodustat, Desidustat, and Enarudustat are the available clinical trial inhibitors. This study is proposed to focus on the repurposing of FDA-approved drugs as effective PHD2 inhibitors. This computational study utilises e-pharmacophore hypothesis generation from the native ligand–protein complex (PDB ID: 5OX6) based on XP visualiser information. The hypothesis containing five essential features (AAANR) was incorporated for FDA database screening, followed by Glide XP molecular docking and Prime MM-GBSA binding free energy calculations. Top scored ligands were investigated and Fenbufen was identified as an effective PHD-2 inhibitor by comparing with the native co-crystal ligand (Vadadustat). The manual lead optimisation of the Fenbufen structure was adopted to improve inhibitory potency, by increasing the binding affinity and protein–ligand stability. The newly designed compounds B and C showed additional binding interactions, excellent docking scores, binding free energy, and an acceptable range of ADME properties. Also, Fenbufen and compound C owned preferable protein–ligand stability during MD simulation when compared with the co-crystallised clinical trial ligand. Based on our findings, we deduce that Fenbufen can be proposed as an effective repurposable candidate as its structural modification showed a remarkable improvement in PHD2 inhibition.Graphical abstract Supplementary informationThe online version contains supplementary material available at 10.1007/s11224-022-02012-z.

Identification of potential matrix metalloproteinase-2 inhibitors from natural products through advanced machine learning-based cheminformatics approaches.

Matrix metalloproteinase-2 (MMP-2) is capable of degrading Collage TypeIV in the vascular basement membrane and extracellular matrix. Studies have shown that MMP-2 is tightly associated with the biological behavior of malignant tumors. Therefore, the identification of inhibitors targeting MMP-2 could be effective in treating the disease by maintaining extracellular matrix homeostasis. In the pharmaceutical and biomedical fields, many computational tools are widely used, which improve the efficiency of the whole process to some extent. Apart from the conventional cheminformatics approaches (e.g., pharmacophore model and molecular docking), virtual screening strategies based on machine learning also have promising applications. In this study, we collected 2871 compound activity data against MMP-2 from the ChEMBL database and divided the training and test sets in a 3:1 ratio. Four machine learning algorithms were then selected to construct the classification models, and the best-performing model, i.e., the stacking-based fusion model with the highest AUC value in both training and test datasets, was used for the virtual screening of ZINC database. Next, we screened 17 potential MMP-2 inhibitors from the results predicted by the machine learning model via ADME/T analysis. The interactions between these compounds and the target protein were explored through molecular docking calculations, and the results showed that ZINC712249, ZINC4270723, and ZINC15858504 had lower binding free energies than the co-crystal ligand. To further examine the binding stability of the complexes, we performed molecular dynamics simulations and finally identified these three hits as the most promising natural products for MMP-2 inhibitors.

Design, synthesis, anticancer evaluation, molecular docking, and in silico ADME analysis of novel chalcones incorporated indole-pyrimidine derivatives as promising anticancer agents

A novel library of aryl rings attached chalcone derivatives of indole-pyrimidines ( 10a-j ) were designed, synthesized, and evaluated for anticancer activities against four human cancer cell lines such as PC3, DU-145 (prostate), A549 (lung), and (MCF-7 (breast) by employing MTT method. The results of the MTT assay showed that all the synthetic compounds had some tumor cell growth inhibitory activities with IC 50 values range from 0.01±0.005 µM to 14.6 ± 6.32 µM, and standard drug with values 1.97 ± 0.45 µM to 3.08 ± 0.135 µM, respectively. Among them, compounds ( 10a, 10b, 10c, 10d , and 10e ) displayed remarkable activities, and out of which compounds 10a and 10d were found to be the most promising with potential anti-cancer activity. Molecular docking studies of the compounds were carried out against SARM (PDB ID: 3V49) and the docking results exclusively proposed binding modes in the active site of SARM. Among all, 10a, 10b, 10d , 10 h and 10j showed comparable dock score, 10a and 10b (-142.89 and -145.13) displayed pronounced interactions when compared with co-crystal ligand (-143.40) . Finally, in silico predictions of ADME and pharmacokinetic parameters indicated that all these compounds could be considered as drug candidates with oral bioavailability.

Toward the Discovery of a Novel Class of Leads for High Altitude Disorders by Virtual Screening and Molecular Dynamics Approaches Targeting Carbonic Anhydrase.

For decades, carbonic anhydrase (CA) inhibitors, most notably the acetazolamide-bearing 1,3,4-thiadiazole moiety, have been exploited at high altitudes to alleviate acute mountain sickness, a syndrome of symptomatic sensitivity to the altitude characterized by nausea, lethargy, headache, anorexia, and inadequate sleep. Therefore, inhibition of CA may be a promising therapeutic strategy for high-altitude disorders. In this study, co-crystallized inhibitors with 1,3,4-thiadiazole, 1,3-benzothiazole, and 1,2,5-oxadiazole scaffolds were employed for pharmacophore-based virtual screening of the ZINC database, followed by molecular docking and molecular dynamics simulation studies against CA to find possible ligands that may emerge as promising inhibitors. Compared to the co-crystal ligands of PDB-1YDB, 6BCC, and 6IC2, ZINC12336992, ZINC24751284, and ZINC58324738 had the highest docking scores of −9.0, −9.0, and −8.9 kcal/mol, respectively. A molecular dynamics (MD) simulation analysis of 100 ns was conducted to verify the interactions of the top-scoring molecules with CA. The system’s backbone revealed minor fluctuations, indicating that the CA–ligand complex was stable during the simulation period. Simulated trajectories were used for the MM-GBSA analysis, showing free binding energies of −16.00 ± 0.19, −21.04 ± 0.17, and −19.70 ± 0.18 kcal/mol, respectively. In addition, study of the frontier molecular orbitals of these compounds by DFT-based optimization at the level of B3LYP and the 6-311G(d,p) basis set showed negative values of the HOMO and LUMO, indicating that the ligands are energetically stable, which is essential for forming a stable ligand–protein complex. These molecules may prove to be a promising therapy for high-altitude disorders, necessitating further investigations.