Pharmacokinetics and drug-likeness of anti-cancer traditional Chinese medicine: molecular docking and molecular dynamics simulation study

MCM7 (Minichromosome Maintenance Complex Component 7) is a component of the DNA replication licensing factor, which controls DNA replication. The MCM7 protein is linked to tumor cell proliferation and has a function in the development of several human cancers. Several types of cancer may be treated by inhibiting the protein, as it is strongly produced throughout this process. Significantly, Traditional Chinese Medicine (TCM), which has a long history of clinical adjuvant use against cancer, is rapidly gaining traction as a valuable medical resource for the development of novel cancer therapies, including immunotherapy. Therefore, the goal of the research was to find small molecular therapeutic candidates against the MCM7 protein that may be used to treat human cancers. A computational-based virtual screening of 36,000 natural TCM libraries is carried out for this goal using a molecular docking and dynamic simulation technique. Thereby, ∼8 novel potent compounds i.e., ZINC85542762, ZINC95911541, ZINC85542617, ZINC85542646, ZINC85592446, ZINC85568676, ZINC85531303, and ZINC95914464 were successfully shortlisted, each having the capacity to penetrate the cell as potent inhibitors for MCM7 to curb this disorder. These selected compounds were found to have high binding affinities compared to the reference (AGS compound) i.e. < -11.0 kcal/mol. ADMET and pharmacological properties showed that none of these 8 compounds poses any toxic property (carcinogenicity) and have anti-metastatic, and anticancer activity. Additionally, MD simulations were run to assess the compounds' stability and dynamic behavior with the MCM7 complex for about 100 ns. Finally, ZINC95914464, ZINC95911541, ZINC85568676, ZINC85592446, ZINC85531303, and ZINC85542646 are identified as highly stable within the complex throughout the 100 ns simulations. Moreover, the results of binding free energy suggested that the selected virtual hits significantly bind to the MCM7 which implied these compounds may act as a potential MCM7 inhibitor. However, in vitro testing protocols are required to further support these results. Further, assessment through various lab-based trial methods can assist with deciding the action of the compound that will give options in contrast to human cancer immunotherapy.Communicated by Ramaswamy H. Sarma.

Investigating the self-assembling of nicotinic hydrazide-based amphiphile into nano-range vesicles and its amphotericin B loading applications

Most of the drugs are hydrophobic and have low water solubility, therefore posing issues in their absorption and bioavailability. Nonionic surfactants improve the solubility of hydrophobic drugs by entrapping them in their lipid bilayers. Two nonionic surfactants NODNH-16 and NODNH-18 are synthesized and characterized using different techniques i.e. EI-MS, ¹H NMR, and FTIR. These newly synthesized surfactants were screened for blood hemolysis assay and cell toxicity studies using the NIH/3T3 cell line to assess their biocompatibility. Then amphotericin B was loaded into niosomal vesicles, and the drug entrapment efficiency of these surfactants was measured using UV-visible spectroscopy. The morphology of drug-loaded niosomes of synthesized surfactants was investigated using AFM, and their size, polydispersity, and zeta potential were measured with the Zetasizer instrument. Finally, a simulation study was performed to determine the pattern of self-assembly of the synthesized amphiphiles. Both synthesized nonionic surfactants showed good entrapment efficiency of 60.65 ± 2.12% and 68.45 ± 2.12%, respectively. It was also confirmed that both these synthesized nonionic surfactants were safe and biocompatible and showed less blood hemolysis (i.e. 21.13 ± 2.11% and 23.32 ± 2.45%) and higher 3T3 cells' viability at 150 µg/mL concentration as compared to Tween®-80. The antifungal potential of amphotericin B-loaded niosomes has been evaluated against unicellular multi-fungal species, which showed a promising potential for fungicidal activity. These results are substantiated by constructing a safe vehicle system for drug delivery.

Integrated Bioinformatics-Based Subtractive Genomics Approach to Decipher the Therapeutic Drug Target and Its Possible Intervention against Brucellosis

Brucella suis, one of the causative agents of brucellosis, is Gram-negative intracellular bacteria that may be found all over the globe and it is a significant facultative zoonotic pathogen found in livestock. It may adapt to a phagocytic environment, reproduce, and develop resistance to harmful environments inside host cells, which is a crucial part of the Brucella life cycle making it a worldwide menace. The molecular underpinnings of Brucella pathogenicity have been substantially elucidated due to comprehensive methods such as proteomics. Therefore, we aim to explore the complete Brucella suis proteome to prioritize the novel proteins as drug targets via subtractive proteo-genomics analysis, an effort to conjecture the existence of distinct pathways in the development of brucellosis. Consequently, 38 unique metabolic pathways having 503 proteins were observed while among these 503 proteins, the non-homologs (n = 421), essential (n = 350), drug-like (n = 114), virulence (n = 45), resistance (n = 42), and unique to pathogen proteins were retrieved from Brucella suis. The applied subsequent hierarchical shortlisting resulted in a protein, i.e., isocitrate lyase, that may act as potential drug target, which was finalized after the extensive literature survey. The interacting partners for these shortlisted drug targets were identified through the STRING database. Moreover, structure-based studies were also performed on isocitrate lyase to further analyze its function. For that purpose, ~18,000 ZINC compounds were screened to identify new potent drug candidates against isocitrate lyase for brucellosis. It resulted in the shortlisting of six compounds, i.e., ZINC95543764, ZINC02688148, ZINC20115475, ZINC04232055, ZINC04231816, and ZINC04259566 that potentially inhibit isocitrate lyase. However, the ADMET profiling showed that all compounds fulfill ADMET properties except for ZINC20115475 showing positive Ames activity; whereas, ZINC02688148, ZINC04259566, ZINC04232055, and ZINC04231816 showed hepatoxicity while all compounds were observed to have no skin sensitization. In light of these parameters, we recommend ZINC95543764 compound for further experimental studies. According to the present research, which uses subtractive genomics, proteins that might serve as therapeutic targets and potential lead options for eradicating brucellosis have been narrowed down.

Reverse vaccinology approach for multi-epitope centered vaccine design against delta variant of the SARS-CoV-2

The ongoing COVID-19 outbreak, initially identified in Wuhan, China, has impacted people all over the globe and new variants of concern continue to threaten hundreds of thousands of people. The delta variant (first reported in India) is currently classified as one of the most contagious variants of SARS-CoV-2. It is estimated that the transmission rate of delta variant is 225% times faster than the alpha variant, and it is causing havoc worldwide (especially in the USA, UK, and South Asia). The mutations found in the spike protein of delta variant make it more infective than other variants in addition to ruining the global efficacy of available vaccines. In the current study, an in silico reverse vaccinology approach was applied for multi-epitope vaccine construction against the spike protein of delta variant, which could induce an immune response against COVID-19 infection. Non-toxic, highly conserved, non-allergenic and highly antigenic B-cell, HTL, and CTL epitopes were identified to minimize adverse effects and maximize the efficacy of chimeric vaccines that could be developed from these epitopes. Finally, V1 vaccine construct model was shortlisted and 3D modeling was performed by refinement, docking against HLAs and TLR4 protein, simulation and in silico expression. In silico evaluation showed that the designed chimeric vaccine could elicit an immune response (i.e., cell-mediated and humoral) identified through immune simulation. This study could add to the efforts of overcoming global burden of COVID-19 particularly the variants of concern.

Nanoparticles Loaded Thermoresponsive In Situ Gel for Ocular Antibiotic Delivery against Bacterial Keratitis

Antibiotics delivered through conventional dosage against ophthalmic infections show lower therapeutic efficacy due to their low residence time. Therefore, there is a great need to design and develop novel dosage forms that would increase the ocular residence time of antibiotics at the site of infection. This study describes the development of nanoparticles laden in situ gelling solution, intended to sustain antibiotic release for improved therapeutic efficiency. Oxytetracycline-loaded gelatin-polyacrylic acid nanoparticles were prepared and incorporated in poloxamer-N407 solution. The rheological properties of the system were studied concerning time and temperature. Moreover, in vivo biocompatibility of the system was ascertained using the Draize test and histological studies. Finally, the optimized formulation was evaluated for in vitro antibacterial activity against one of the most common keratitis causing bacteria, Pseudomonas aeruginosa. Additionally, the in vivo efficacy was evaluated on the rabbit’s eye conjunctivitis model. The formulation showed a sustained effect against keratitis; furthermore, the antibacterial activity was comparable with the commercial product.

Differential analysis of Orientia tsutsugamushi genomes for therapeutic target identification and possible intervention through natural product inhibitor screening

Orientia tsutsugamushi (Ott) is a causative agent of scrub typhus, and one of the emerging pathogens that could affect a large human population. It is one of the misdiagnosed and under-reported, febrile illnesses that infects various body organs (skin, heart, lung, kidney, and brain). The control of this infection is hampered due to the lack of drugs or vaccine against it. This study was undertaken to identify potential drug targets from the core genome of Ott and investigate novel natural product inhibitors against them. Hence, the available genomes for 22 strains of Ott were downloaded from the PATRIC database, and pan-genomic analysis was performed. Only 202 genes were present in the core region. Among these, 94 were identified as essential, 32 non-homologous to humans, nine non-homologous to useful gut flora and a single gene dapD as a drug target. Product of this gene (2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase) was modeled and docked against traditional Indian (Ayurvedic) and Chinese phytochemical libraries, with best hits selected for docking, based on multiple target-drug/s interactions and minimum energy scores. ADMET profiling and molecular dynamics simulation was performed for top three compounds from each library to assess the toxicity and stability, respectively. We presume that these compounds (ZINC8214635, ZINC32793028, ZINC08101133, ZINC85625167, ZINC06018678, and ZINC13377938) could be successful inhibitors of Ott. However, in-depth experimental and clinical research is needed for further validation.

Identification of a Novel Therapeutic Target against XDR Salmonella Typhi H58 Using Genomics Driven Approach Followed Up by Natural Products Virtual Screening

Typhoid fever is caused by a pathogenic, rod-shaped, flagellated, and Gram-negative bacterium known as Salmonella Typhi. It features a polysaccharide capsule that acts as a virulence factor and deceives the host immune system by protecting phagocytosis. Typhoid fever remains a major health concern in low and middle-income countries, with an estimated death rate of ~200,000 per annum. However, the situation is exacerbated by the emergence of the extensively drug-resistant (XDR) strain designated as H58 of S. Typhi. The emergence of the XDR strain is alarming, and it poses serious threats to public health due to the failure of the current therapeutic regimen. A relatively newer computational method called subtractive genomics analyses has been widely applied to discover novel and new drug targets against pathogens, particularly drug-resistant ones. The method involves the gradual reduction of the complete proteome of the pathogen, leading to few potential and novel drug targets. Thus, in the current study, a subtractive genomics approach was applied against the Salmonella XDR strain to identify potential drug targets. The current study predicted four prioritized proteins (i.e., Colanic acid biosynthesis acetyltransferase wcaB, Shikimate dehydrogenase aroE, multidrug efflux RND transporter permease subunit MdtC, and pantothenate synthetase panC) as potential drug targets. Though few of the prioritized proteins are treated in the literature as the established drug targets against other pathogenic bacteria, these drug targets are identified here for the first time against S. Typhi (i.e., S. Typhi XDR). The current study aimed at drawing attention to new drug targets against S. Typhi that remain largely unexplored. One of the prioritized drug targets, i.e., Colanic acid biosynthesis acetyltransferase, was predicted as a unique, new drug target against S. Typhi XDR. Therefore, the Colanic acid was further explored using structure-based techniques. Additionally, ~1000 natural compounds were docked with Colanic acid biosynthesis acetyltransferase, resulting in the prediction of seven compounds as potential lead candidates against the S. Typhi XDR strain. The ADMET properties and binding energies via the docking program of these seven compounds characterized them as novel drug candidates. They may potentially be used for the development of future drugs in the treatment of Typhoid fever.

Pan-Genome Reverse Vaccinology Approach for the Design of Multi-Epitope Vaccine Construct against Escherichia albertii

Escherichia albertii is characterized as an emerging pathogen, causing enteric infections. It is responsible for high mortality rate, especially in children, elderly, and immunocompromised people. To the best of our knowledge, no vaccine exists to curb this pathogen. Therefore, in current study, we aimed to identify potential vaccine candidates and design chimeric vaccine models against Escherichia albertii from the analysis of publicly available data of 95 strains, using a reverse vaccinology approach. Outer-membrane proteins (n = 4) were identified from core genome as vaccine candidates. Eventually, outer membrane Fimbrial usher (FimD) protein was selected as a promiscuous vaccine candidate and utilized to construct a potential vaccine model. It resulted in three epitopes, leading to the design of twelve vaccine constructs. Amongst these, V6 construct was found to be highly immunogenic, non-toxic, non-allergenic, antigenic, and most stable. This was utilized for molecular docking and simulation studies against six HLA and two TLR complexes. This construct can therefore be used for pan-therapy against different strains of E. albertii and needs to be tested in vitro and in vivo.

Molecular cloning, expression, and characterization of E2F transcription factor 4 from Antheraea pernyi

The E2F transcription factor family is distributed widely in eukaryotes and has been well studied among mammals. In the present study, the E2F transcription factor 4 (E2F4) gene was isolated from fat bodies of Antheraea pernyi and sequenced. E2F4 comprised a 795 bp open reading frame encoding a deduced amino acid sequence of 264 amino acid residues. The recombinant protein was expressed in Escherichia coli (Transetta DE3), and anti-E2F4 antibodies were prepared. The deduced amino acid sequence displayed significant homology to an E2F4-like protein from Bombyx mori L. Quantitative real-time polymerase chain reaction analysis revealed that E2F4 expression was highest in the integument, followed by the fat body, silk glands, and haemocytes. The expression of E2F4 was upregulated in larvae challenged by bacterial (Escherichia coli, Micrococcus luteus), viral (nuclear polyhedrosis virus), and fungal (Beauveria bassiana) pathogens. These observations indicated that E2F4 is an inducible protein in the immune response of A. pernyi and probably in other insects.

Hydrogen chromate PVC matrix membrane sensor for potentiometric determination of chromium(III) and chromium(VI) ions

A novel potentiometric Cr(6+) PVC matrix membrane sensor incorporating nickel tris(1,10-bathophenanthroline) hydrogen chromate as an electroactive material and 2-nitrophenyl phenyl ether as solvent mediator is described. In a phosphate buffer solution of pH 5, the sensor displays a rapid and linear response for Cr(6-) over the concentration range 2 x 10(-2)-8 x 10(-6) M with an anionic slope of 55.5 +/- 0.2 mV decade(-1) and a detection limit of the order of 0.4 microg ml(-1). The sensor is used for sequential determination of Cr(6+) and Cr(3+) by direct monitoring of Cr(6+) followed by oxidation of Cr(3+) and measurement of the total chromium. The average recoveries of Cr(3+) and Cr(6+) at concentration levels of 0.5-50 microg ml(-1) are 98.1 +/- 0.4% and 99.1 +/- 0.4% respectively. Redox and precipitation titrations involving Cr(6+) as a titrant are monitored with the sensor. Cr(3+) and/or Cr(6+) in wastewaters of some industries (e.g., leather tanning, electroplating, aluminum painting) and the chromium contents of some alloys and refractory bricks are assessed. The results agree fairly well with data obtained using the standard diphenylcarbazide spectrophotometric method.

A Novel Membrane Sensor for Histamine H1-Receptor Antagonist "Fexofenadine"

The construction and general performance of thirteen new polymeric membrane sensors for the determination of fexofenadine hydrochloride based on its ion exchange with reineckate, tetraphenylborate and tetraiodomercurate have been studied. The effects of membrane composition, type of plasticizer, pH value of sample solution and concentration of the analyte in the sensor internal solution have been thoroughly investigated. The novel sensor based on reineckate exchanger shows a stable, potentiometric response for fexofenadine in the concentration range of 1 x 10(-2) - 2.5 x 10(-6) M at 25 degrees C that is independent of pH in the range of 2.0 - 4.5. The sensor possesses a Nernstian cationic slope of 62.3+/-0.7 mV/concentration decade and a lower detection limit of 1.3 x 10(-6) M with a fast response time of 20 - 40 s. Selectivity coefficients for a number of interfering ions and excipients relative to fexofenadine were investigated. There is negligible interference from almost all studied cations, anions, and pharmaceutical excipients, however, citrizine that has a structure homologous to that of fexofenadine was found to interfere. The determination of fexofenadine in aqueous solution shows an average recovery of 99.83% with a mean relative standard deviation (RSD) of 0.5%. Direct potentiometric determination of fexofenadine in tablets gave results that compare favorably with those obtained by standard spectrophotometric methods. Potentiometric titration of fexofenadine with phosphomolybdic acid as a titrant has been monitored with the proposed sensor as an end point indicator electrode.

Gallamine-tetraphenylborate-modified carbon paste electrode for the potentiometric determination of gallamine triethiodide (flaxedil)

The construction and general performance of a novel modified carbon paste electrode for the determination of gallamine triethiodide have been developed. The electrode shows a stable, potentiometric response for gallamine in the concentration range 1 x 10(-3)-2 x 10(-6) M at 25 degrees C independent of pH in the range 5-8. The electrode passes a near-Nernstian cationic slope of 17.0+/-0.7 mV and lower detection limit of 1 x 10(-6) M with a fast response time of 20-45 s. Selectivity coefficients for gallamine relative to a number of interfering substances were investigated. There is a negligible interference from the studied cations, anions, and pharmaceutical excipients. The determination of gallamine in aqueous solution shows an average recovery of 99.5% and a mean relative standard deviation (RSD) of 1.4% at 100 microg/ml. The direct determination of gallamine in injection solution gave results that compare favorably with those obtained by the British pharmacopoeia method. Potentiometric titration of gallamine with sodium tetraphenylborate and phosphotungstic acid as a titrant has been monitored with the modified carbon paste electrode as an end-point indicator electrode.