Screening Of Potential Inhibitors Research Articles

Screening Potential Nitrification Inhibitors through a Structure–Activity Relationship Study—The Case of Cinnamic Acid Derivatives

Using a nitrification inhibitor to decrease nitrification rates in soil represents a promising strategy to improve nitrogen fertilizer use efficiency. Nonetheless, rapid screening of nitrification inhibitors remains challenging. In this study, we propose a strategy to screen potential nitrification inhibitors through a structure–activity relationship (SAR) study based on a rapid determination of nitrification inhibition. To demonstrate this, the nitrification inhibition potentials of cinnamic acid derivatives against Nitrosomonas europaea growth were evaluated in a liquid culture. The SAR study showed that hydroxyl and fluoride groups were the favorable substituents on the benzene ring, and the ester group and double bond in the side chain were essential for maintaining high inhibition efficacy. Three compounds with notable inhibitory efficacy (EC50 = 8–25 μM) were further assessed in agricultural soil, and they displayed a noteworthy reduction in nitrification rate and bacterial amoA gene numbers. Based on the results, we identified methyl cinnamate, methyl 4-hydroxycinnamate, and methyl 4-fluorocinnamate as promising candidates for nitrification inhibition.

Screening Potential Nitrification Inhibitors through a Structure–Activity Relationship Study—The Case of Cinnamic Acid Derivatives

Using a nitrification inhibitor to decrease nitrification rates in soil represents a promising strategy to improve nitrogen fertilizer use efficiency. Nonetheless, rapid screening of nitrification inhibitors remains challenging. In this study, we propose a strategy to screen potential nitrification inhibitors through a structure–activity relationship (SAR) study based on a rapid determination of nitrification inhibition. To demonstrate this, the nitrification inhibition potentials of cinnamic acid derivatives against Nitrosomonas europaea growth were evaluated in a liquid culture. The SAR study showed that hydroxyl and fluoride groups were the favorable substituents on the benzene ring, and the ester group and double bond in the side chain were essential for maintaining high inhibition efficacy. Three compounds with notable inhibitory efficacy (EC50 = 8–25 μM) were further assessed in agricultural soil, and they displayed a noteworthy reduction in nitrification rate and bacterial amoA gene numbers. Based on the results, we identified methyl cinnamate, methyl 4-hydroxycinnamate, and methyl 4-fluorocinnamate as promising candidates for nitrification inhibition.

Rutin attenuates ensartinib-induced hepatotoxicity by non-transcriptional regulation of TXNIP

Ensartinib, an approved ALK inhibitor, is used as a first-line therapy for advanced ALK-positive non-small cell lung cancer in China. However, the hepatotoxicity of ensartinib seriously limits its clinical application and the regulatory mechanism is still elusive. Here, through transcriptome analysis we found that transcriptional activation of TXNIP was the main cause of ensartinib-induced liver dysfunction. A high TXNIP level and abnormal TXNIP translocation severely impaired hepatic function via mitochondrial dysfunction and hepatocyte apoptosis, and TXNIP deficiency attenuated hepatocyte apoptosis under ensartinib treatment. The increase in TXNIP induced by ensartinib is related to AKT inhibition and is mediated by MondoA. Through screening potential TXNIP inhibitors, we found that the natural polyphenolic flavonoid rutin, unlike most reported TXNIP inhibitors can inhibit TXNIP by binding to TXNIP and partially promoting its proteasomal degradation. Further studies showed rutin can attenuate the hepatotoxicity of ensartinib without antagonizing its antitumor effects. Accordingly, we suggest that TXNIP is the key cause of ensartinib-induced hepatotoxicity and rutin is a potential clinically safe and feasible therapeutic strategy for TXNIP intervention.Graphical

Fluorescent assay for acetylcholinesterase activity and inhibitor screening based on lanthanide organic/inorganic hybrid materials.

It is of great significance for the clinical diagnosis of Alzheimer's disease (AD) to achieve the on-site activity evaluation of acetylcholinesterase (AChE), the hydrolase of acetylcholine (ACh). Herein, we have developed a biosensing method endowed with considerable superiority based on the organic-inorganic hybrid composite Eu(DPA)3@Lap with excellent stability and fluorescent properties for this purpose by loading Eu3+ ions and 2,6-dipicolinic acid (DPA) into LAPONITE® (Lap). Through the comprehensive consideration of the specific hydrolysis of acetylthiocholine (ATCh) into thiocholine (TCh) by AChE, the high binding affinity of TCh to copper ion (Cu2+), and the selective fluorescence quenching ability of Cu2+, a simple Eu(DPA)3@Lap-based assay was developed to realize the rapid and convenient evaluation of AChE activity. Owning to the facile signal on-off-on response mode with a clear PET-based sensing mechanism, our assay presents favorable selectivity and sensitivity (LOD of 0.5 mU mL-1). Furthermore, the fluorescent assay was successfully applied for assessing AChE activity in human serum samples and screening potential AChE inhibitors, showing potential for application in the early diagnosis and drug screening of AD, as a new development path of AD therapy.

Screening of potential inhibitors against structural proteins from Monkeypox and related viruses of Poxviridae family via docking and molecular dynamics simulation

Monkeypox virus (MPXV) is an orthopoxvirus which causes zoonotic infection in humans. Even though sporadic cases of this infection are limited to the African continent, but if the infection continues to increase unabated, it can be a cause of serious concern for the human populace. Smallpox vaccination has been in use against monkeypox infection but it only provides mild protection. In the current study, we have screened novel small molecules (estrone fused heterocycles (EH1-EH7)) exhibiting good binding with monkeypox virus protein and related proteins from Poxviridae family of viruses via computational approaches. EH1-7 series of small molecules selected for the work have been synthesized via cycloaddition methodology. Docking and Molecular Dynamics (MD) results highlight EH4 compound to have strong binding affinity towards monkeypox and other related viral proteins selected for the study. Thus, computational outcomes suggest EH4 as a good candidate against monkeypox. Currently, no antiviral medication has been approved against monkeypox and the treatment is only via therapeutics available for smallpox and related conditions that may be helpful against monkeypox. Our study is thus an attempt to screen novel compounds against monkeypox infection, which would, in turn, facilitate development of novel therapeutics against Poxviridae family. HIGHLIGHTS Monkeypox infection is a public health emergency and necessitates immediate drug discovery. Molecular docking study to screen estrone-fused heterocycles compounds against Monkeypox and other orthopoxviruses. Molecular dynamics simulations revealed interaction/high binding affinities among EH4 heterocyclic compound and profilin-like protein from the monkeypox virus. Estrone-fused heterocycles compounds are promising anti-viral agents as per our in silico analysis. Our study provides evidence for investigating estrone-fused heterocycles compounds for further pharmacological interventions. Communicated by Ramaswamy H. Sarma

Construction of a Dendritic Nanoassembly-Based Fluorescent Biosensor for Electrostatic Interaction-Independent and Label-Free Measurement of Human Poly(ADP-ribose) Polymerase 1 in Lung Tissues.

Poly(ADP-ribose) polymerase 1 (PARP-1) is responsible for catalyzing the creation of poly(ADP-ribose) polymer and involved in DNA replication and repair. Sensitive measurement of PARP-1 is critical for clinical diagnosis. However, the conventional electrostatic attraction-based PAPR-1 assays usually involve laborious procedures, poor sensitivity, and false positives. Herein, we demonstrate the construction of a dendritic nanoassembly-based fluorescent biosensor for electrostatic interaction-independent and label-free measurement of human PARP-1 in lung tumor tissues. When PARP-1 is present, the specific double-stranded DNA (dsDNA)-activated PARP-1 transfers the ADP-ribosyl group from nicotinamide adenine dinucleotide (NAD+)/biotinylated NAD+ to the PARP-1 itself, resulting in the formation of biotinylated dsDNA-PARP-1-PAR polymer bioconjugates that can be captured by magnetic beads. Upon the addition of TdT, APE1, and NH2-modified T-rich probe, the captured dsDNAs with dual 3'-OH termini initiate TdT-activated APE1-mediated hyperbranched amplification to produce abundant dendritic DNA nanoassemblies that can be stained by SYBR Green I to generate a high fluorescence signal. This biosensor is characterized by a template-free, electrostatic interaction-independent, high sensitivity, and label-free assay. It enables rapid (less than 3 h) measurement of PARP-1 with a limit of detection of 4.37 × 10-8 U/μL and accurate measurement of cellular PARP-1 activity with single-cell sensitivity. Moreover, it is capable of screening potential inhibitors and discriminating the PARP-1 level in normal person tissues and lung cancer patient tissues, with great potential in PARP-1-related clinical diagnosis and drug discovery.

An automated analysis method enabling the screening of covalent thrombin and factor XIIa inhibitors via liquid chromatography-mass spectrometry.

An automated sample preparation and separation method for the analysis of various enzyme-inhibitor combinations using liquid chromatography (LC) coupled to mass spectrometry (MS) is presented. As conventional anticoagulants have several drawbacks, the most severe being the elevated risk of internal bleedings, it is necessary to develop new-generation anticoagulants with reduced side effects. Therefore, the screening of potential inhibitors against anticoagulation targets like thrombin and FXIIa is important to design a potent and selective inhibitor. To facilitate the analysis of numerous enzyme-inhibitor covalent complexes, automation of the analysis using an LC system with a user-defined injection sequence is helpful. The developed method ensures comparable reaction conditions like reaction time and temperature for all enzyme-inhibitor complexes. Furthermore, it prevents time-consuming manual sample preparation and potential manual errors. To achieve good reproducibility with relative standard deviation of approximately 3% for three-fold determination, multiple cleaning steps were added to the automated sample preparation. Subsequently, this method was applied to screen a variety of 15 aminopyrazole- and aminotriazole-based inhibitors with a covalent mechanism of action against thrombin and to test two covalent inhibitors for FXIIa. Successful complex formation and acylation of the catalytic center of the enzymes was monitored using deconvoluted mass spectra and the matching mass shifts of the acyl moiety of the analyzed inhibitors. The inhibitors' structure directly influenced reaction yields. Sterically demanding aminotriazoles and acyl moieties both affected the product formation negatively. However, the screening yielded several promising candidates for new covalent thrombin inhibitors, which might find their application as prospective anticoagulants.

Analytical assays to evaluate enzymatic activity and screening of inhibitors for ornithine decarboxylase

Ornithine decarboxylase (ODC) catalyzes the decarboxylation of ornithine to produce putrescine, the first step in the metabolism of polyamines (putrescine, spermidine, and spermine), which are essential growth factors in eukaryotic cells. ODC is active as a homodimer and depends on pyridoxal 5′-phosphate (PLP) as a cofactor. An increase in the concentration of polyamines has been associated with carcinogenesis. Therefore, there is much interest in identifying inhibitors of this pathway as potential chemotherapeutic and chemopreventive agents. The best-known inhibitor of mammalian ODC is α-difluoromethylornithine (DFMO), a highly selective compound that alkylates Cys-360 (a residue of the ODC active site). Although DFMO was initially developed for the treatment of cancer, the World Health Organization recommends its use in combination with nifurtimox for the treatment of human African trypanosomiasis. Considering the importance of ODC as a promising target for the treatment of various types of cancer and other infectious diseases, choosing the right method for screening potential inhibitors can help to accelerate the discovery of new drugs. Several methods for the determination of ODC activity are found in the literature. Among these, we can mention analysis with radioactive markers, colorimetric assays using auxiliary enzymes to detect CO2 or H2O2 release, chromatographic separations with putrescine derivatization, mass spectrometry, and spectroscopic techniques. In this review, the main analysis methods used will be described, highlighting their advantages and disadvantages, as well as identifying the most promising methods for high-throughput screening.

Tannic acid-aminopropyltriethoxysilane co-deposition modified polymer membrane for α-glucosidase immobilization

Mussel-inspired catechol-amine co-deposition is an effective modification strategy for various materials. In this work, polyvinylidene fluoride (PVDF) membrane was employed as the carrier for α-glucosidase immobilization. By virtue of the co-polymerization of tannic acid (TA) and 3-aminopropyltriethoxysilane (APTES) and the hydrolysis of APTES, a hierarchical layer-colloidal nanospheres coating was decorated on the surface of PVDF membrane. Subsequently, α-glucosidase was covalently bound to the modified PVDF membrane through Schiff base reaction and Michael addition reaction between the residual quinine groups in the coating and the amino groups in enzyme molecules. Several parameters affecting the immobilization procedure were investigated thoroughly. The morphology and functional groups of the prepared composite were characterized by scanning electron microscopy (SEM), Fourier transform infrared-Attenuated total reflectance spectroscopy (FTIR-ATR), and X-ray photoelectron spectroscopy (XPS). Combined with capillary electrophoresis (CE) analysis, the performance, enzyme reaction kinetics and inhibition kinetics of PVDF-immobilized α-glucosidase were studied. The immobilized enzyme exhibited the enhanced tolerance to temperature and pH value. In addition, it possessed good reusability maintaining 77.1% of initial relative activity after 11 recycles, and batch-to-batch reproducibility with RSD of 4.3% (n = 10). The Michaelis-Menten constant (Km) of immobilized enzyme was calculated to be 4.16 mM, and IC50 value of acarbose was 0.10 µM. Finally, the PVDF-immobilized α-glucosidase was applied to screening potential inhibitors from 13 kinds of traditional Chinese medicines (TCMs), among which Sanguisorba Radix exhibited the strongest inhibitory activity. The positive results suggested that TA/APTES co-deposition was a simple and mild functionalization method for chemically inert polymer membrane and the proposed screening method was a reliable approach for discovering enzyme inhibitors from TCMs.

Fluorinated Phosphoadenosine 5'-Phosphosulfate Analogues for Continuous Sulfotransferase Activity Monitoring and Inhibitor Screening by 19F NMR Spectroscopy.

Sulfotransferases (STs) are ubiquitous enzymes that participate in a vast number of biological processes involving sulfuryl group (SO3) transfer. 3′-phosphoadenosine 5′-phosphosulfate (PAPS) is the universal ST cofactor, serving as the “active sulfate” source in cells. Herein, we report the synthesis of three fluorinated PAPS analogues that bear fluorine or trifluoromethyl substituents at the C2 or C8 positions of adenine and their evaluation as substitute cofactors that enable ST activity to be quantified and real-time-monitored by fluorine-19 nuclear magnetic resonance (19F NMR) spectroscopy. Using plant AtSOT18 and human SULT1A3 as two model enzymes, we reveal that the fluorinated PAPS analogues show complementary properties with regard to recognition by enzymes and the working 19F NMR pH range and are attractive versatile tools for studying STs. Finally, we developed an 19F NMR assay for screening potential inhibitors against SULT1A3, thereby highlighting the possible use of fluorinated PAPS analogues for the discovery of drugs for ST-related diseases.

Phosphopantetheinyl transferase binding and inhibition by amidino-urea and hydroxypyrimidinethione compounds

Owing to their role in activating enzymes essential for bacterial viability and pathogenicity, phosphopantetheinyl transferases represent novel and attractive drug targets. In this work, we examined the inhibitory effect of the aminido-urea 8918 compound against the phosphopantetheinyl transferases PptAb from Mycobacterium abscessus and PcpS from Pseudomonas aeruginosa, two pathogenic bacteria associated with cystic fibrosis and bronchiectasis, respectively. Compound 8918 exhibits inhibitory activity against PptAb but displays no activity against PcpS in vitro, while no antimicrobial activity against Mycobacterium abscessus or Pseudomonas aeruginosa could be detected. X-ray crystallographic analysis of 8918 bound to PptAb-CoA alone and in complex with an acyl carrier protein domain in addition to the crystal structure of PcpS in complex with CoA revealed the structural basis for the inhibition mechanism of PptAb by 8918 and its ineffectiveness against PcpS. Finally, in crystallo screening of potent inhibitors from the National Cancer Institute library identified a hydroxypyrimidinethione derivative that binds PptAb. Both compounds could serve as scaffolds for the future development of phosphopantetheinyl transferases inhibitors.

The Molecular Biology of Phosphodiesterase 4 Enzymes as Pharmacological Targets: An Interplay of Isoforms, Conformational States, and Inhibitors.

The phosphodiesterase 4 (PDE4) enzyme family plays a pivotal role in regulating levels of the second messenger cAMP. Consequently, PDE4 inhibitors have been investigated as a therapeutic strategy to enhance cAMP signaling in a broad range of diseases, including several types of cancers, as well as in various neurologic, dermatological, and inflammatory diseases. Despite their widespread therapeutic potential, the progression of PDE4 inhibitors into the clinic has been hampered because of their related relatively small therapeutic window, which increases the chance of producing adverse side effects. Interestingly, the PDE4 enzyme family consists of several subtypes and isoforms that can be modified post-translationally or can engage in specific protein-protein interactions to yield a variety of conformational states. Inhibition of specific PDE4 subtypes, isoforms, or conformational states may lead to more precise effects and hence improve the safety profile of PDE4 inhibition. In this review, we provide an overview of the variety of PDE4 isoforms and how their activity and inhibition is influenced by post-translational modifications and interactions with partner proteins. Furthermore, we describe the importance of screening potential PDE4 inhibitors in view of different PDE4 subtypes, isoforms, and conformational states rather than testing compounds directed toward a specific PDE4 catalytic domain. Lastly, potential mechanisms underlying PDE4-mediated adverse effects are outlined. In this review, we illustrate that PDE4 inhibitors retain their therapeutic potential in myriad diseases, but target identification should be more precise to establish selective inhibition of disease-affected PDE4 isoforms while avoiding isoforms involved in adverse effects. SIGNIFICANCE STATEMENT: Although the PDE4 enzyme family is a therapeutic target in an extensive range of disorders, clinical use of PDE4 inhibitors has been hindered because of the adverse side effects. This review elaborately shows that safer and more effective PDE4 targeting is possible by characterizing 1) which PDE4 subtypes and isoforms exist, 2) how PDE4 isoforms can adopt specific conformations upon post-translational modifications and protein-protein interactions, and 3) which PDE4 inhibitors can selectively bind specific PDE4 subtypes, isoforms, and/or conformations.

Screening and testing potential inhibitors of sulphide gas production by sulphate-reducing bacteria.

Sulphate-reducing bacteria are commonly associated with biological causes of oil well souring. Biosulphetogenesis can directly affect oil quality and storage due to the accumulation of sulphides. In addition, these microorganisms can create bio-incrustation that can clog pipes. Sulphite reductase (SIR) is the enzyme responsible for converting ion sulphite into sulphide and several substances may interfere or control such activity. This interference can hinder growth of the sulphate-reducing bacteria and, consequently, it reduces sulphide accumulation in situ. This work focuses on molecular modelling techniques along with in vitro experiments in order to investigate the potential of two essential oils and one vegetable oil as main inhibitors of sulphite reductase activity. Docking simulation identified several substances present in Rosmarinus officinalis, Tea tree and Neem extractable oils as potential inhibitors of SIR. Substances present in Neem vegetable oil are the most potent inhibitors, followed by Rosmarinus officinalis and Tea tree essential oils. The Neem oil mixture showed a superior effectiveness in intracellular SIR inhibitory effects.

Structural based screening of potential inhibitors of SMAD4: a step towards personalized medicine for gall bladder and other associated cancers

Gall bladder cancer (GBC) is an aggressive and most common malignancy of biliary tract lacking effective treatment due to unavailability of suitable biomarkers and therapeutics. SMAD4 is an essential mediator of transforming growth factor-β pathway involved in various cellular processes like growth, differentiation and apoptosis and also recognized as therapeutic target for GBC and other gastrointestinal tract cancers. In the present study, 3D structure of SMAD4 mutants was optimized through molecular dynamics simulation (MDS) along with wildtype. Furthermore, binding site of protein was predicted through hybrid approach and structural based virtual screening against two drug libraries was performed followed by docking. MDS of top docking score protein-ligand complexes were carried, and binding free energy was rescored. Two potential inhibitors, namely ZINC2098840 and ZINC8789167, were screened that displayed higher binding affinity towards mutant proteins compared with wildtype and both hydrophilic as well as hydrophobic interactions play a crucial role during protein-ligand binding. Current study identified novel and potent inhibitors of SMAD4 mutant that could be used as a drug candidate for the development of personalized medicine for gall bladder and other associated cancers.

A controlled T7 transcription-driven symmetric amplification cascade machinery for single-molecule detection of multiple repair glycosylases.

Genomic oxidation and alkylation are two of the most important forms of cytotoxic damage that may induce mutagenesis, carcinogenicity, and teratogenicity. Human 8-oxoguanine (hOGG1) and alkyladenine DNA glycosylases (hAAG) are responsible for two major forms of oxidative and alkylative damage repair, and their aberrant activities may cause repair deficiencies that are associated with a variety of human diseases, including cancers. Due to their complicated catalytic pathways and hydrolysis mechanisms, simultaneous and accurate detection of multiple repair glycosylases has remained a great challenge. Herein, by taking advantage of unique features of T7-based transcription and the intrinsic superiorities of single-molecule imaging techniques, we demonstrate for the first time the development of a controlled T7 transcription-driven symmetric amplification cascade machinery for single-molecule detection of hOGG1 and hAAG. The presence of hOGG1 and hAAG can remove damaged 8-oxoG and deoxyinosine, respectively, from the dumbbell substrate, resulting in breaking of the dumbbell substrate, unfolding of two loops, and exposure of two T7 promoters simultaneously. The T7 promoters can activate symmetric transcription amplifications with the unfolded loops as the templates, inducing efficient transcription to produce two different single-stranded RNA transcripts (i.e., reporter probes 1 and 2). Reporter probes 1 and 2 hybridize with signal probes 1 and 2, respectively, to initiate duplex-specific nuclease-directed cyclic digestion of the signal probes, liberating large amounts of Cy3 and Cy5 fluorescent molecules. The released Cy3 and Cy5 molecules can be simply measured by total internal reflection fluorescence-based single-molecule detection, with the Cy3 signal indicating the presence of hOGG1 and the Cy5 signal indicating the presence of hAAG. This method exhibits good specificity and high sensitivity with a detection limit of 3.52 × 10−8 U μL−1 for hOGG1 and 3.55 × 10−7 U μL−1 for hAAG, and it can even quantify repair glycosylases at the single-cell level. Moreover, it can be applied for the measurement of kinetic parameters, the screening of potential inhibitors, and the detection of repair glycosylases in human serum, providing a new paradigm for repair enzyme-related biomedical research, drug discovery, and clinical diagnosis.

Simultaneous Detection of Tyrosine and Structure-Specific Intrinsic Fluorescence in the Fibrillation of Alzheimer's Associated Peptides.

Understanding of the structural changes during their aggregation and interaction is a prerequisite for establishing the precise clinical relevance of human islet amyloid polypeptide (hIAPP) (involved in Type-II Diabetes Mellitus) in the treatment of Alzheimer's disease stemmed from beta-amyloid (Aβ). Herein, we show that the steady-state emission spectra obtained from photoluminescence (PL) simultaneously capture both the tyrosine derivative (tyrosinate) and the structure-specific intrinsic fluorescence during the aggregation of Aβ and hIAPP. We observe multiple peaks in the emission spectra which exist for structure-specific intrinsic fluorescence, and use the second derivative UV-Vis spectra and the shift in the tyrosine peak as a quantitative measure of the dissimilitude in the electronic states and the fibril growth. We further applied these techniques to detect the static electric field (0, 40, 120, 200 V/cm) induced promotion and inhibition of fibrillation in Aβ, hIAPP and their electric field dependent role in the fibrillation of Aβ : hIAPP(1 : 1). The results were corroborated by field-emission scanning electron microscopy (FESEM), and the determinations of secondary structures by Fourier transform infrared spectroscopy (FTIR). The results indicate that the emission spectrum can be used as a sensor to detect the presence of fibrils; hence for screening potential inhibitors of amyloid fibrillation.

Adsorbed hollow fiber immobilized tyrosinase for the screening of enzyme inhibitors from Pueraria lobata extract

In this study, a method based on adsorbed hollow fiber immobilized tyrosinase (TYR) was developed to screening potential TYR inhibitors from Pueraria lobate extract. Kojic acid and ranitidine were used as positive and negative control to verify the reliability of the proposed method, respectively. Several significant parameters of the screening process, including the amount of P. lobata extract, adsorption time and incubation time, were optimized. After investigating the repeatability of the developed method, seven potential active compounds in P. lobata extract were successfully detected and their chemical structures were tentatively identified by liquid chromatography – mass spectrometry analysis. Furthermore, the inhibitory activity of four identified compounds on TYR was tested in vitro, and three of them, namely, puerarin, puerarin-6″-O-xyloside and puerarin apioside were verified to have good TYR inhibitory activity with IC50 value of 478.5, 513.8, and 877.3 μM, respectively. In addition, the molecular docking results indicated that these compounds could bind to the amino acid residues in TYR catalytic pocket. These results proved that the proposed method is a feasible approach for screening of TYR inhibitors from plant extract.

In silico design and analysis of NS4B inhibitors against hepatitis C virus

The hepatitis C virus is a communicable disease that gradually harms the liver leading to cirrhosis and hepatocellular carcinoma. Important therapeutic interventions have been reached since the discovery of the disease. However, its resurgence urges the need for new approaches against this malady. The NS4B receptor is one of the important proteins for Hepatitis C Virus RNA replication that acts by mediating different viral properties. In this work, we opt to explore the relationships between the molecular structures of biologically tested NS4B inhibitors and their corresponding inhibitory activities to assist the design of novel and potent NS4B inhibitors. For that, a set of 115 indol-2-ylpyridine-3-sulfonamides (IPSA) compounds with inhibitory activity against NS4B is used. A hybrid genetic algorithm combined with multiple linear regressions (GA-MLR) was implemented to construct a predictive model. This model was further used and applied to a set of compounds that were generated based on a pharmacophore modeling study combined with virtual screening to identify structurally similar lead compounds. Multiple filtrations were implemented for selecting potent hits. The selected hits exhibited advantageous molecular features, allowing for favorable inhibitory activity against HCV. The results showed that 7 out of 1285 screened compounds, were selected as potent candidate hits where Zinc14822482 exhibits the best predicted potency and pharmacophore features. The predictive pharmacokinetic analysis further justified the compounds as potential hit molecules, prompting their recommendation for a confirmatory biological evaluation. We believe that our strategy could help in the design and screening of potential inhibitors in drug discovery. Communicated by Ramaswamy H. Sarma

Cloning, functional characterization and screening of potential inhibitors for Chilo partellus chitin synthase A using in silico, in vitro and in vivo approaches

Chitin synthase (CHS) is one of the crucial enzymes that play an essential role in chitin synthesis during the molting process, and it is considered to be the specific target to control insect pests. Currently, there are no potent inhibitors available in the market, which specifically target this enzyme. Pyrimidine nucleoside peptide, nikkomycin Z, binds to nucleotide-binding sites of fungal and insect CHS. But, their mode of action is still fragmentary due to the lack of a 3Dstructure of CHS. Chilo partellus is a severe pest insect of major food crops such as maize and sorghum, in an attempt to target integument expressed cuticular CpCHS. The CpChsA cDNA was cloned, and subsequently, their developmental and tissue-specific expression was studied. The 3D structure of the CHS catalytic domain was modeled, after which natural compounds were screened using a virtual screening workflow and resulted in the identification of five hit molecules. Molecular dynamics simulations were performed to investigate the dynamics and interactions of hits with CpCHS. The obtained results revealed that the compounds kasugamycin, rutin and robinin could act as potent inhibitors of CpCHS. All three molecules were observed to significantly reduce the chitin production as validated using in vitro and in vivo studies. Thus, this study aims to provide a set of novel inhibitor molecules against CpCHS for controlling the pest population. Communicated by Ramaswamy H. Sarma

Screening of potential inhibitors against flotillin-1 as therapeutics for Alzheimer's disease

Background: Alzheimer's disease (AD) is one of the most common neurological disorders occurring in older people. So far, no specific drug is available for the disease, and only palliative medicines are available for the patients. Accumulation of amyloid beta (Aβ) peptides is considered to play a crucial role in the generation of the disease. Aβ peptide is generated by the proteolysis of amyloid precursor protein by two distinct proteases β and γ-secretase. Flotillin-1 (FLOT1) directly binds to the cytoplasmic tail of β-secretase and affects the sorting and recycling of the enzyme. Increased expression of FLOT1 has been correlated with the progression of AD, while FLOT1 knockdown causes a reduction in Aβ production. Thus, FLOT1 is an attractive therapeutic target for the suppression of beta-secretase 1 (BACE-1 ). Objective: This study aims to screen the potential inhibitors against FLOT1 as therapeutics for AD. Materials and Methodology: In this work, protein–protein interactions, tertiary structure prediction, molecular docking, and molecular dynamics (MD) simulation were performed. Results: Tertiary structure prediction of FLOT1 and screening inhibitors against it helped in finding key molecules with potential therapeutic properties. Protein–protein interaction study of FLOT1 deciphered the interactors playing key role in AD. Pharmacokinetic parameters were quantified for each potential inhibitor. The results of MD simulation analysis revealed that the ZINC67911837 had better inhibitory activities with FLOT1. Conclusion: The analysis suggests that the ZINC67911837 compound could be a novel potential inhibitor of FLOT1 to modulate BACE-1 activity and used as a therapeutic agent for the treatment of AD. This study facilitates the initiation of the natural drug discovery process for the treatment of AD patients.