QSAR modeling, docking and ADMET studies for exploration of potential anti-malarial compounds against Plasmodium falciparum

Screening of phytochemicals from Clerodendrum inerme (L.) Gaertn as potential anti-breast cancer compounds targeting EGFR: an in-silico approach

Breast cancer (BC) is the most prevalent malignancy among women around the world. The epidermal growth factor receptor (EGFR) is a tyrosine kinase receptor (RTK) of the ErbB/HER family. It is essential for triggering the cellular signaling cascades that control cell growth and survival. However, perturbations in EGFR signaling lead to cancer development and progression. Hence, EGFR is regarded as a prominent therapeutic target for breast cancer. Therefore, in the current investigation, EGFR was targeted with phytochemicals from Clerodendrum inerme (L.) Gaertn (C. inerme). A total of 121 phytochemicals identified by gas chromatography-mass spectrometry (GC-MS) analysis were screened against EGFR through molecular docking, ADMET analyses (Absorption, Distribution, Metabolism, Excretion, and Toxicity), PASS predictions, and molecular dynamics simulation, which revealed three potential hit compounds with CIDs 10586 [i.e. alpha-bisabolol (-6.4 kcal/mol)], 550281 [i.e. 2,(4,4-Trimethyl-3-hydroxymethyl-5a-(3-methyl-but-2-enyl)-cyclohexene) (-6.5 kcal/mol)], and 161271 [i.e. salvigenin (-7.4 kcal/mol)]. The FDA-approved drug gefitinib was used to compare the inhibitory effects of the phytochemicals. The top selected compounds exhibited good ADMET properties and obeyed Lipinski's rule of five (ROF). The molecular docking analysis showed that salvigenin was the best among the three compounds and formed bonds with the key residue Met 793. Furthermore, the molecular mechanics generalized born surface area (MMGBSA) calculations, molecular dynamics simulation, and normal mode analysis validated the binding affinity of the compounds and also revealed the strong stability and compactness of phytochemicals at the docked site. Additionally, DFT and DOS analyses were done to study the reactivity of the compounds and to further validate the selected phytochemicals. These results suggest that the identified phytochemicals possess high inhibitory potential against the target EGFR and can treat breast cancer. However, further in vitro and in vivo investigations are warranted towards the development of these constituents into novel anti-cancer drugs.

Experimental and theoretical studies on antituberculosis activity of different benzimidazole derivatives

Tuberculosis (TB) continues to be one of the deadliest infectious diseases with a rapid increase in multidrug-resistant cases. The discovery of new agents against tuberculosis is urgently needed. Thus, the research article focuses on the antituberculosis activity of a series of benzimidazolium compounds. The antituberculosis activities of compounds including benzimidazole core (7a-h) against Mycobacterium tuberculosis H37Rv strain were tested in vitro using the BACTEC MGIT 960 system. The concentrations of benzimidazole compounds were adjusted to range from 0.25 to 4 μg/ml. The antituberculosis interactions of the compounds were investigated by molecular docking and molecular dynamics simulation. The results revealed that only benzimidazolium salt 7h showed antituberculosis activity at MIC value of 2 μg/ml although the other compounds showed no antituberculosis activity. The docking data revealed that 7h could bind to InhA thus indicating its inhibition potential on the enzyme. Molecular dynamics simulation exhibited that 7h formed a stable complex with the enzyme and was able to remain inside the binding region of the enzyme. Besides, the pharmacokinetic and drug-likeness properties of the compounds were assessed through computational approaches. The compounds exhibited drug-like properties. Consequently, 7h could be a good candidate for the development of new TB drugs.

Multitargeted molecular docking and dynamics simulation studies of 1,3,4-thiadiazoles synthesised from (R)-carvone against specific tumour protein markers: An In-silico study of two diastereoisomers

In the present work, we describe the synthesis of new 1,3,4-thiadiazole derivatives from natural (R)-carvone in three steps including, dichloro-cyclopropanation, a condensation with thiosemicarbazide and then a 1,3-dipolar cycloaddition reaction with various nitrilimines. the targeted compounds were structurally identified by 1H & 13C NMR and HRMS analyses. The cytotoxic assay demonstrated that some synthesized novel compounds were potent on certain cancer cell lines. Molecular modeling studies were undertaken to rationalize the wet lab study results. Furthermore, molecular docking was performed to unveil the binding potential of the most active derivatives, 3a and 6c, to caspase-3 and COX-2. The stabilities of the protein-compound complexes obtained from the docking were evaluated using MD simulation. Furthermore, FMO and related parameters of the active compounds and their stereoisomers were examined through DFT studies. The docking study showed compound 6c had a higher binding potential than caspase-3. However, the binding strength of 6c was found to be less than that of the standard drug, doxorubicin, as it formed lower conventional hydrogen bonds. On the other hand, compound 3a had a higher binding potential to COX-2. However, the binding potential 3a was much lower than that of the standard COX-2 inhibitor, celecoxib. The MD simulation demonstrated that the caspase-3-6c complex was less stable than the caspase-3-doxorubicin complex. In contrast, the COX-2-3a complex was stable, and 3a was anticipated to remain inside the protein's binding pocket. The DFT study showed that 3a had higher chemical stability than 6c. The electron exchange capacity, chemical stability, and molecular orbital distributions of the stereoisomers of the active compounds were also found to be alike.

Integrated computational and experimental evaluation of phenolic constituents of Apricot fruit L. for antiqourum sensing, antibiofilm, antioxidant, and 15-lox inhibitory properties

The present study investigated the antioxidant profile together with the antibacterial potential of Apricot L. with the aim to find a functional food based anti-infective lead. Additionally the study evaluated the biofilm and QS inhibitory potential of the plant using Pseudomonas aeruginosa (ATCC 15442) and Chromo bacterium Violaceum (DSM 30191) respectively. Several fractions of the peel of Apricot were subjected to initial antimicrobial and antibiofilm screening. Among all the fractions, methanol and ethyl acetate fractions displayed significant antimicrobial activity against the strains selected with MIC values 1.25 mg/dL and 1.68 mg/dL respectively. Similarly, while evaluating antiqourum-sensing potential, methanol extract showed remarkable zone of inhibition (14mm) with Violaceum inhibition (58%) while aqueous part presented moderately good inhibition (32%) with zone of inhibition of (4mm). N-hexane fraction was least active in this regard. In case of free radicals scavenging aptitudes, Ethanolic fraction displayed the highest free radicals scavenging potential (IC50μg/mL 13.76 ± 23.61) while Aqueous and ethyl acetate part exhibited moderate to good antioxidant behaviors with IC50μg/mL of 26.74 ± 22.00 and 19.49 ± 2.91 respectively. Then the selected compounds were screened for putative binding sites and molecular docking studies followed by enzyme inhibition assays. The negative binding energies and close proximity to residues in the binding pocket of selected targets including human α- soybean lox (PDB ID 1IK3), quorum sensing regulators LasR (2UV0) were observed which indicated high affinity and tight binding capacity of compounds 1 and 5 towards the active sites of LasR 2UV0 and 15-lipoxygenase. The physicochemical characteristics and toxicity expectation were computationally accomplished. Bioactivity prediction study revealed that all of the selected Phytoconstituents displayed incredible Bioactivity score. None of the selected chemical compound was found to be toxic as discovered by toxicity studies. Compound 4 exhibited the highest inhibition of 15-lipoxygenase in vitro (69%, at 0.037 mM final concentration) and that is accompanied by compound 5 (60%) whereas in the biofilm inhibition assay, compound 1 was most active (IC50 0.05 mM), followed by compound 3 (IC50 0.07 mM). It was therefore determined that compounds 1 and 3 had the highest biofilm inhibitory activity, whereas compounds 4 and 5 were potent 15-lipoxygenase inhibitors with potentially anti-inflammatory properties. Future investigations are suggested for the characterization and formulation development.

Synthesis, characterization, antiproliferative activity, docking, and molecular dynamics simulation of new 1,3-dihydro-2H-benzimidazol-2-one derivatives

Cancer is a global public health problem that affects millions each year. Novel anticancer drug candidates are in need to treat various cancers and to overcome the resistance that exists against drugs in use. Benzimidazole derivatives have been reported as anticancer agents. These lead us to synthesize similar benzimidazole derivatives and investigate their anticancer activity. In this study, six new 1,3-dihydro-2H-benzimidazol-2-one-based molecules (2a-f) were synthesized. The structures of these molecules were verified by spectroscopic methods. The antiproliferative activities of molecules 2a-f were screened against a panel of human cancer cell lines, including the liver, colon, lung, and breast. The molecules were also tested towards normal human lung cell line to determine their selectivity. The results demonstrated that compound 2d had the highest cytotoxic effect compared to compounds 2a-c, 2e, and 2f against DLD-1 and MDA-MB-231 cell lines. The binding potential of the relatively active compound, 2d, with three targets was investigated through molecular docking. The stability of target-compound complexes procured from the docking was explored through molecular dynamics (MD) simulation. The docking and MD simulation studies revealed that compound 2d had the highest potential to bind to GALR3 among the targets. Furthermore, the computational pharmacokinetic study demonstrated that the synthesized compounds had drug-like properties.Communicated by Ramaswamy H. Sarma.

Synthesis, Spectral Characterization, Thermal Investigation, Computational Studies, Molecular Docking, and In Vitro Biological Activities of a New Schiff Base Derived from 2-Chloro Benzaldehyde and 3,3'-Dimethyl-[1,1'-biphenyl]-4,4'-diamine

The current research involves the synthesis of a new Schiff base through the reaction between 2-chlorobenzaldehyde and 3,3'-dimethyl-[1,1'-biphenyl]-4,4'-diamine by using a natural acid catalyst and a synthesized compound physicochemically characterized by X-ray diffraction, Fourier transform infrared spectroscopy, 1H- and 13C-nuclear magnetic resonance, and liquid chromatography-mass spectrometry. Thermal studies were conducted using thermogravimetric, differential thermal analysis, and differential thermogravimetric curves. These curves were obtained in an inert nitrogen environment from ambient temperature to 1263 K using heating rates of 10, 15, and 20 K·min-1. Using thermocurve data, model-free isoconversional techniques such as Kissinger-Akahira-Sunose, Flynn-Wall-Ozawa, and Friedman are used to determine kinetic parameters. These parameters include activation energy, phonon frequency factor, activation enthalpy, activation entropy, and Gibb's free energy change. All of the results have been thoroughly investigated. The molecule's anti-inflammatory and antidiabetic properties were also examined. To learn more about the potential of the Schiff base and how successfully it can suppress the amylase enzyme, a molecular docking experiment was also conducted. For in silico research, the Swiss Absorption, Distribution, Metabolism, Excretion, and Toxicity algorithms were used to calculate the theoretical pharmacokinetic properties, oral bioavailability, toxic effects, and biological activities of the synthesized molecule. Moreover, the cytotoxicity tests against a human lung cancer cell line (A549) using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay demonstrated that the synthesized Schiff base exhibited significant anticancer properties.

Novel hybrids of thiazolidinedione-1,3,4-oxadiazole derivatives: synthesis, molecular docking, MD simulations, ADMET study, in vitro, and in vivo anti-diabetic assessment

As compared to standard medicinal compounds, hybrid molecules that contain multiple biologically active functional groups have greater affinity and efficiency. Hence based on this concept, we predicted that a combination of thiazolidinediones and 1,3,4-oxadiazoles may enhance α-amylase and α-glucosidase inhibition activity. A series of novel 3-((5-phenyl-1,3,4-oxadiazol-2-yl)methyl)thiazolidine-2,5-dione derivatives (5a-5j) were synthesized and characterized using different spectroscopic techniques i.e., FTIR, 1H-NMR, 13C-NMR and MS. To evaluate in silico, molecular docking, MMGBSA, and MD simulations were carried out which were further evaluated via in vitro inhibition of α-amylase and α-glycosidase enzyme inhibition assays. In addition, the in vivo study was performed on a genetic model of Drosophila melanogaster to assess the antihyperglycemic effects. The compounds (5a-5j) demonstrated α-amylase and α-glucosidase inhibitory activity in the range of IC50 values 18.42 ± 0.21-55.43 ± 0.66 μM and 17.21 ± 0.22-51.28 ± 0.88 μM respectively when compared to standard acarbose. Based on the in vitro studies, compounds 5a, 5b, and 5j were found to be potent against both enzymes. In vivo studies have shown that compounds 5a, 5b, and 5j lower glucose levels in Drosophila. These compounds could be further developed in the future to produce a new class of antidiabetic agents.

Computer-aided drug design combined network pharmacology to explore anti-SARS-CoV-2 or anti-inflammatory targets and mechanisms of Qingfei Paidu Decoction for COVID-19

Introduction

Coronavirus Disease-2019 (COVID-19) is an infectious disease caused by SARS-CoV-2. Severe cases of COVID-19 are characterized by an intense inflammatory process that may ultimately lead to organ failure and patient death. Qingfei Paidu Decoction (QFPD), a traditional Chines e medicine (TCM) formula, is widely used in China as anti-SARS-CoV-2 and anti-inflammatory. However, the potential targets and mechanisms for QFPD to exert anti-SARS-CoV-2 or anti-inflammatory effects remain unclear.

Methods

In this study, Computer-Aided Drug Design was performed to identify the antiviral or anti-inflammatory components in QFPD and their targets using Discovery Studio 2020 software. We then investigated the mechanisms associated with QFPD for treating COVID-19 with the help of multiple network pharmacology approaches.

Results and discussion

By overlapping the targets of QFPD and COVID-19, we discovered 8 common targets (RBP4, IL1RN, TTR, FYN, SFTPD, TP53, SRPK1, and AKT1) of 62 active components in QFPD. These may represent potential targets for QFPD to exert anti-SARS-CoV-2 or anti-inflammatory effects. The result showed that QFPD might have therapeutic effects on COVID-19 by regulating viral infection, immune and inflammation-related pathways. Our work will promote the development of new drugs for COVID-19.

Molecular Docking, Validation, Dynamics Simulations, and Pharmacokinetic Prediction of Phytochemicals Isolated From Croton dichogamus Against the HIV-1 Reverse Transcriptase

The human immunodeficiency virus (HIV) infection and the associated acquired immune deficiency syndrome (AIDS) remain global challenges even after decades of successful treatment, with eastern and southern Africa still bearing the highest burden of disease. Following a thorough computational study, we report top 10 phytochemicals isolated from Croton dichogamus as potent reverse transcriptase inhibitors. The pentacyclic triterpenoid, aleuritolic acid (L12) has displayed best docking pose with binding energy of -8.48 kcal/mol and Ki of 0.61 μM making it superior in binding efficiency when compared to all docked compounds including the FDA-approved drugs. Other phytochemicals such as crotoxide A, crothalimene A, crotodichogamoin B and crotonolide E have also displayed strong binding energies. These compounds could further be investigated as potential antiretroviral medication.

Virtual screening and molecular dynamic simulations of the antimalarial derivatives of 2-anilino 4-amino substituted quinazolines docked against a Pf-DHODH protein target

Background

The processes of drug development and validation are too expensive to be subjected to experimental trial and errors. Hence, the use of the insilico approach becomes imperative. To this effect, the drug-likeness and pharmacokinetic properties of the ten (10) previously designed derivatives of 2-anilino 4-amino substituted quinazolines were carried out. Their predicted ligand binding interactions were also carried out by docking them against the Plasmodium falciparum dihydroorotate dehydrogenase (Pf-DHODH) protein target, and the stability of the complex was determined through dynamic simulations. The drug-likeness and pharmacokinetic characteristics were estimated using the online SwissADME software, while the Molegro Virtual Docker (MVD) software was used for molecular docking. And the dynamic simulation was performed for the duration of 100 ns to verify the stability of the docked complex, with the aid of a Schrödinger program, Desmond.

Results

The designed derivatives were all found to pass the Lipinski test of drug likeness, while the pharmacokinetic studies result that the skin permeability and molar refractivity values of the derivatives are both within the limits. In addition, except for derivative C-01, most of the derivatives have strong gastrointestinal absorptions and lack Pgp substrate. Furthermore, no derivative inhibited CYP1A2, CYP2C9, or CYP2C19. The docking studies show the better binding affinities between the ligands and Pf-DHODH than those between the atovaquone or chloroquine standards. The derivative C-02, {5-((6,7-dimethoxy-4-((3-nitrobenzyl)amino)quinazolin-2-yl)amino)-2-fluorobenzaldehyde} was found to be the most stable derivative, with a re-rank docking score of - 173.528 kcal/mol and interaction energy of - 225.112 kcal/mol. The dynamic simulation analysis shows that the derivative C-02 forms a stable complex with the protein target over the simulation time.

Conclusions

The ability of these ligands to form hydrogen bonds, as well as various other interactions, was cited as a factor responsible for their better binding affinity. These findings could aid further the development of enhanced antimalarial drugs.

Synthesis, Antimicrobial Activity, and Molecular Modeling Studies of Some Benzoxazole Derivatives

Background:

The need to develop novel antimicrobial agents is apparent as infectious diseases are increasing and resistance is rapidly developing against the drugs used in the treatment.

Objective:

This study aimed at the synthesis, antimicrobial susceptibility testing, and computational elucidation of the mechanism of action of benzoxazole derivatives. It also aimed to compare the results obtained in this study with the previous studies by our group. This would pave the way for designing novel molecules with better antimicrobial activity. The other goal was pharmacophore analysis and in silico ADMET analysis of them.

Methods:

In this study, synthesis, antimicrobial susceptibility testing, molecular docking, pharmacophore analysis, and ADMET prediction were carried out.

Results:

The antimicrobial activity studies demonstrated that the synthesized compounds were active against standard strains and clinical isolates at high concentrations. Then, the antimicrobial testing results were compared to similar benzoxazoles tested by our group previously. Benzoxazole derivatives without a methylene bridge between oxazole and phenyl ring were found to be more active than those with the methylene bridge. This was also confirmed by molecular modeling undertaken in this study. The computational results indicated that the antibacterial activity could be achieved by DNA gyrase inhibition. Pharmacophore analysis showed that hydrogen bond acceptor (HBA), hydrogen bond donor (HBD), and hydrophobicity features would contribute to the inhibition. In addition, in silico ADMET property investigation of the compounds exhibited that they had the desired pharmacokinetics.

Conclusion:

Although antibacterial activity by inhibiting DNA gyrase is selective, the synthesized compounds were active at much higher concentrations than the standards. Therefore, in prospective antimicrobial studies, it is better to focus on benzoxazole derivatives without the methylene bridge. Since the compounds had suitable in silico ADMET properties, screening them against the other pharmacologic activities should be carried out. It is recommended to support the molecular modeling results with in vitro or in vivo studies.

A Rapid Assessment Model for Liver Toxicity of Macrolides and an Integrative Evaluation for Azithromycin Impurities

Impurities in pharmaceuticals of potentially hazardous materials may cause drug safety problems. Macrolide antibiotic preparations include active pharmaceutical ingredients (APIs) and different types of impurities with similar structures, and the amount of these impurities is usually very low and difficult to be separated for toxicity evaluation. Our previous study indicated that hepatotoxicity induced by macrolides was correlated with c-fos overexpression. Here, we report an assessment of macrolide-related liver toxicity by ADMET prediction, molecular docking, structure–toxicity relationship, and experimental verification via detection of the c-fos gene expression in liver cells. The results showed that a rapid assessment model for the prediction of hepatotoxicity of macrolide antibiotics could be established by calculation of the -CDOCKER interaction energy score with the FosB/JunD bZIP domain and then confirmed by the detection of the c-fos gene expression in L02 cells. Telithromycin, a positive compound of liver toxicity, was used to verify the correctness of the model through comparative analysis of liver toxicity in zebrafish and cytotoxicity in L02 cells exposed to telithromycin and azithromycin. The prediction interval (48.1∼53.1) for quantitative hepatotoxicity in the model was calculated from the docking scores of seven macrolide antibiotics commonly used in clinics. We performed the prediction interval to virtual screening of azithromycin impurities with high hepatotoxicity and then experimentally confirmed by liver toxicity in zebrafish and c-fos gene expression. Simultaneously, we found the hepatotoxicity of azithromycin impurities may be related to the charge of nitrogen (N) atoms on the side chain group at the C5 position via structure–toxicity relationship of azithromycin impurities with different structures. This study provides a theoretical basis for improvement of the quality of macrolide antibiotics.

Chemical profile and antiperiodontal potential of Thymus linearis Benth. Essential oil using ADMET prediction, In silico and in vitro tools

Periodontitis is an important health concern that is associated with long term complications. Development of resistance to antibiotics limits the treatment options in periodontitis. We investigated Thymus linearis essential oil for treatment of periodontitis. The essential oil was collected using hydrodistillation and characterized using GC-MS. The constituents were further analyzed for druglikeness, ADMET properties and molecular docking using transcription regulators 2UV0 and 3QP5. The GC-MS results revealed that carvacrol was a major constituent (76.26%) followed by caryophyllene oxide (6.83%) and L-borneol (6.08%). The in vitro antimicrobial studies showed significant inhibition against Staphylococcus aureus, Staphylococcus epidermidis and Pseudomonas aeruginosa (MIC range 0.024 –0.312μg/mL). The essential oil showed a good inhibition of bacterial biofilm produced by S. aureus (72%) and S. epidermidis (70%). Finally, the antiquorum sensing property (30 mm zone of inhibition) was recorded with violacein inhibition (58%). Based on in silico and in vitro findings, it was concluded that T. linearis essential oil can be used for the treatment of periodontal infections.

Antifungal activity and mechanism of action of 2-chloro-N -phenylacetamide: a new molecule with activity against strains of Aspergillus flavus

Aspergillus genus causes many diseases, and the species Aspergillus flavus is highly virulent. Treatment of aspergillosis involves azole derivatives such as voriconazole and polyenes such as amphotericin B. Due to an increase in fungal resistance, treatments are now less effective; the search for new compounds with promising antifungal activity has gained importance. The aims of this study were to evaluate the effects of the synthetic amide 2-chloro-N-phenylacetamide (A1Cl) against strains of Aspergillus flavus and to elucidate its mechanism of action. Thus, the minimum inhibitory concentration, minimum fungicidal concentration, conidial germination, associations with antifungal agents, cell wall activities, membrane activities and molecular docking were evaluated. A1Cl presented antifungal activity against Aspergillus flavus strains with a minimum inhibitory concentration of between 16 and 256 μg/mL and a minimum fungicidal concentration between 32 and 512 μg/mL. The minimum inhibitory concentration of A1Cl also inhibited conidial germination, but when associated with amphotericin B and voriconazole, it promoted antagonistic effects. Binding to ergosterol on the fungal plasma membrane is the likely mechanism of action, along with possible inhibition of DNA synthesis through the inhibition of thymidylate synthase. It is concluded that the amide 2-chloro-N-phenylacetamide has promising antifungal potential.

Computational prediction of small molecules with predicted binding to FGFR3 and testing biological effects in bone cells

Activating anabolic receptor-mediated signaling is essential for stimulating new bone formation and for promoting bone healing in humans. Fibroblast growth factor receptor (FGFR) 3 is reported to be an important positive regulator of osteogenesis. Presently, recombinant proteins are used to stimulate FGFR3 function but have limitations for therapy due to expense and stability. Therefore, there is a need for identification of novel small molecules binding to FGFR3 that promote biological function. In silico molecular docking and high-throughput virtual screening on zinc database identified seven compounds predicted to bind to an active site within the βC'-βE loop, specific to FGFR3. All seven compounds fall within an acceptable range of ADME/T properties. Four compounds showed a 30-65% oral absorption rate. Density functional theory analysis revealed a high HOMO-LUMO gap, reflecting high molecular stability for compounds 14977614 and 13509082. Five compounds exhibited mutagenicity, while the other three compounds presented irritability. Computational mutagenesis predicted that mutating G322 affected compound binding to FGFR3. Molecular dynamics simulation revealed compound 14977614 is stable in binding to FGFR3. Furthermore, compound 14977614, with an oral absorption rate of 60% and high molecular stability, produced significant increases in both proliferation and differentiation of bone marrow stromal cells in vitro. Anti-FGFR3 treatment completely blocked the stimulatory effect of 14977614 on BMSC proliferation. Ex vivo treatment of mouse calvaria in organ culture for seven days with 14977614 increased mineralization and expression levels of bone formation markers. In conclusion, computational analyses identified seven compounds that bind to the FGFR3, and in vitro studies showed that compound 14977614 exerts significant biological effects on osteogenic cells.

Computer-based identification of potential compounds from Salviae miltiorrhizae against Neirisaral adhesion A regulatory protein

In silico studies are attracting considerable interest due to their ability to understand protein-ligand interactions at the atomic level. The main principal tools of this in silico analyses are molecular docking and molecular dynamic (MD) simulation. This paper examines how can natural compounds that are derived from Salviae miltiorrhizae to block Neisseria adhesion A Regulatory protein (NadR). In molecular docking analysis, only four compounds were found in higher binding affinity with NadR among 10 candidates (tanshinol B, tanshinol A, lithospermic acid and tournefolal were -7.61, -7.56, -8.22 and -7.81 kcal/mol, respectively, compared to -7.23 kcal/mol of native ligand). Absorption, distribution, metabolism, excretion (ADME) and toxicity properties, medicinal chemistry profile, and physicochemical features were displayed that tournefolal contains good properties to work as a safe and good anti-adhesive drug. Therefore, the complexes of these four ligands with NadR protein were subjected to 100 ns of MD simulation. RMSD, RMSF, RG and hydrogen bonding exhibited that tournefolal showed stable binding affinity and molecular interaction with NadR protein. In light of these results, there is now a need to conduct much more in vitro and in vivo studies about the efficacy of tournefolal.Communicated by Ramaswamy H. Sarma.

A Proline-Based Tectons and Supramolecular Synthons for Drug Design 2.0: A Case Study of ACEI

Proline is a unique, endogenous amino acid, prevalent in proteins and essential for living organisms. It is appreciated as a tecton for the rational design of new bio-active substances. Herein, we present a short overview of the subject. We analyzed 2366 proline-derived structures deposited in the Cambridge Structure Database, with emphasis on the angiotensin-converting enzyme inhibitors. The latter are the first-line antihypertensive and cardiological drugs. Their side effects prompt a search for improved pharmaceuticals. Characterization of tectons (molecular building blocks) and the resulting supramolecular synthons (patterns of intermolecular interactions) involving proline derivatives, as presented in this study, may be useful for in silico molecular docking and macromolecular modeling studies. The DFT, Hirshfeld surface and energy framework methods gave considerable insight into the nature of close inter-contacts and supramolecular topology. Substituents of proline entity are important for the formation and cooperation of synthons. Tectonic subunits contain proline moieties characterized by diverse ionization states: -N and -COOH(-COO-), -N+ and -COOH(-COO-), -NH and -COOH(-COO-), -NH+ and -COOH(-COO-), and -NH2+ and -COOH(-COO-). Furthermore, pharmacological profiles of ACE inhibitors and their impurities were determined via an in silico approach. The above data were used to develop comprehensive classification, which may be useful in further drug design studies.

Liver toxicity of macrolide antibiotics in zebrafish

Macrolide antibiotics (macrolides) are among the most commonly prescribed antibiotics worldwide and are used for a wide range of infections, but macrolides also expose people to the risk of adverse events include hepatotoxicity. Here, we report the liver toxicity of macrolides with different structures in zebrafish. The absorption, distribution, metabolism, excretion and toxicology (ADMET) parameters of macrolide compounds were predicted and contrasted by utilizing in silico analysis. Fluorescence imaging and Oil Red O stain assays showed all the tested macrolide drugs induced liver degeneration, changed liver size and liver steatosis in larval zebrafish. Through RNA-seq analysis, we found seven co-regulated differentially expressed genes (co-DEGs) associated with metabolism, apoptosis and immune system biological processes, and two co-regulated significant pathways including amino sugar and nucleotide sugar metabolism and apoptosis signaling pathway. We found that only fosab of seven co-DEGs was in the two co-regulated significant pathways. fosab encoded proto-oncogene c-Fos, which was closely associated with liver diseases. The whole-mount in situ hybridization showed high transcription of c-Fos induced by macrolide compounds mainly in the liver region of zebrafish larvae. Cell Counting Kit-8 (CCK-8) and lactate dehydrogenase (LDH) leakage assays revealed that macrolides exerts significant cytotoxic effects on L02 cells. qRT-PCR and western blot analysis demonstrated macrolides also promoted human c-Fos expression in L02 cells. The c-Fos overexpression significantly reduced cell viability by using CCK-8 assay. These data indicate that hepatotoxicity induced by macrolides may be correlated with c-Fos expression activated by these compounds. This study may provide a biomarker for the further investigations on the mechanism of hepatotoxicity induced by macrolide drugs with different structures, and extend our understanding for improving rational clinical application of macrolides.

Exploration of copy number variation in genes related to anti-malarial drug resistance in Plasmodium falciparum

Development of drug resistance in P. falciparum is one of the major problems associated with malaria treatment. Parasite genetic factors such as single nucleotide polymorphisms (SNPs) and copy number variations (CNV) have shown their role in drug resistance. Most of the studies have focused on the role of SNPs and drug resistance in parasite. However, it has also been shown that CNV is associated with adaptation and drug resistance in parasite. Hence, exploration of copy number polymorphism in essential genes of P. falciparum and their role in anti-malarial resistance is important. This review provides the recent information related to genetic profile of CNV marker in plasmepsin and other genes associated with drugresistanceinP. falciparum. It may be suggested that CNVs in plasmepsin genes are the major driver of piperaquine resistance. Moreover, CNVs in pfcrt and pfmdr1genes appear to play important role in adaptation and hence survival of the parasite. It may be hypothesized that targeting of CNV formation in the parasite could be beneficial for breakdown of its adaption in response to drug pressure.

Ensemble-Based Modeling of Chemical Compounds with Antimalarial Activity

Background:

Malaria or Paludism is a tropical disease caused by parasites of the Plasmodium genre and transmitted to humans through the bite of infected mosquitos of the Anopheles genre. This pathology is considered one of the first causes of death in tropical countries and, despite several existing therapies, they have a high toxicity. Computational methods based on Quantitative Structure- Activity Relationship studies have been widely used in drug design work flows.

Objective:

The main goal of the current research is to develop computational models for the identification of antimalarial hit compounds.

Materials and Methods:

For this, a data set suitable for the modeling of the antimalarial activity of chemical compounds was compiled from the literature and subjected to a thorough curation process. In addition, the performance of a diverse set of ensemble-based classification methodologies was evaluated and one of these ensembles was selected as the most suitable for the identification of antimalarial hits based on its virtual screening performance. Data curation was conducted to minimize noise. Among the explored ensemble-based methods, the one combining Genetic Algorithms for the selection of the base classifiers and Majority Vote for their aggregation showed the best performance.

Results:

Our results also show that ensemble modeling is an effective strategy for the QSAR modeling of highly heterogeneous datasets in the discovery of potential antimalarial compounds.

Conclusion:

It was determined that the best performing ensembles were those that use Genetic Algorithms as a method of selection of base models and Majority Vote as the aggregation method.

In silico ADME and Toxicity Prediction of Ceftazidime and Its Impurities

To improve the quality control of drugs, we predicted the absorption, distribution, metabolism, excretion, and toxicity (ADMET) of ceftazidime (CAZ) and its impurities via in silico methods. We used three types of quantitative structure-activity relationship and docking software for precise prediction: Discovery Studio 4.0, OECD QSAR Toolbox 4.1, Toxtree, and the pkCSM approach. The pharmacokinetics and toxicity of ceftazidime and impurity A (Δ-2-CAZ) are similar. The biological properties of impurity B (CAZ E-isomer) are different from CAZ. Therefore, we focused on drug stability to analyze impurity B. Impurities D and I have strong lipophilicity, good intestinal absorption, and poor excretion in the body. Impurity D is particularly neurotoxic and genotoxic. It is important to control the content of impurity D. The toxicity of impurity F is low, but the toxicity is enhanced when it becomes the C-3 side chain of CAZ and forms a quaternary amine group. We conclude that the beta-lactam ring of nucleus, the quaternary amine group at the C-3 side chain, and the acetates at the C-7 side chain of CAZ are the main toxic functional groups. Impurities B and D may be the genetic impurity in CAZ and may also have neurotoxicity. This in silico approach can predict the toxicity of other cephalosporins and impurities.