Molecular modeling of novel 2-aminopyridine derivatives as potential JAK2 inhibitors: a rational strategy for promising anticancer agents.

Janus kinase 2(JAK2) is a potential target for anticancer drugs in the treatment of numerous myeloproliferative diseases due to its central role in the JAK/STAT signaling cascade. In this study, the binding behavior of 2 amino-pyridine derivatives as JAK2 inhibitors was investigated by using multifaceted strategies including 3D-QSAR, molecular docking, Fingerprint analysis, MD simulations, and MM-PBSA calculations. A credible COMFA (q2 = 0.606 and r2 = 0.919) and COMSIA (q2 = 0.641 and r2 = 0.992) model was developed, where the internal and external validation revealed that the obtained 3D-QSAR models could be capable of predicting bioactivities of JAK2 inhibitors. The structural criteria provided by the contour maps of model were used to computationally develop more potent 100 new JAK2 inhibitors. Docking studies were conducted on the model data set and newly developed compounds (in-house library) to demonstrate their binding mechanism and highlight the key interacting residues within JAK2 active site. The selected docked complexes underwent MD simulation (100 ns), which contributed in the further study of the binding interactions. Binding free energy analyses (MMGB/PBSA) revealed that key residues such as Glu930, Leu932 (hinge region), Asp939 (solvent accessible region), Arg980, Asn981and Asp994 (catalytic site) have a significantly facilitate ligand-protein interactions through H-bonding and van der Waals interactions. The preliminary in-silico ADMET evaluation revealed encouraging results for all the modeled and in-house library compounds. The findings of this research have the potential to offer valuable recommendations for the advancement of novel, potent, and efficacious JAK2 inhibitors. Overall, this work has successfully employed a wide range of computer-based methodologies to understand the interaction dynamics between 2-amino-pyridine derivatives and the JAK2 enzyme, which is a crucial target in myeloproliferative disorders.Communicated by Ramaswamy H. Sarma.

3D-QSAR, docking and molecular dynamics simulations of novel Pyrazolo-pyridazinone derivatives as covalent inhibitors of FGFR1: a scientific approach for possible anticancer agents.

Developing highly potent covalent inhibitors of Fibroblast growth factor receptors 1 (FGFR1) has always been a challenging task. In the current study, various computational techniques, such as 3D-QSAR, covalent docking, fingerprinting analysis, MD simulation followed by MMGB/PBSA, and per-residue energy decomposition analysis were used to explore the binding mechanism of pyrazolo[3,4-d]pyridazinone derivatives to FGFR1. The high q2 and r2 values for the CoMFA and CoMSIA models, suggest that the constructed 3D-QSAR models could reliably predict the bioactivities of FGFR1 inhibitors. The structural requirements revealed by the model's contour maps were strategically used to computationally create an in-house library of more than 100 new FGFR1 inhibitors using the R-group exploration technique implemented in the SparkTM software. The compounds from the in-house library were also mapped in the 3D-QSAR model that predicts comparable pIC50 values with the experimental values. A comparison between 3D-QSAR generated contours and molecular docking conformation of ligands was performed to reveal the fundamentals to design potent FGFR1 covalent inhibitors. The estimated binding free energies (MMGB/PBSA) for the selected compounds were in agreement with the experimental value ranking of their binding affinities towards FGFR1. Furthermore, per-residue energy decomposition analysis has identified Arg627 and Glu531 to contribute significantly in improved binding affinity of compound W16. During ADME analysis, the majority of in-house library compounds exhibited pharmacokinetic properties superior to those of experimentally produced compounds. These new compounds may help researchers better understand FGFR1 inhibition and lead to the creation of novel, potent FGFR1 inhibitors.Communicated by Ramaswamy H. Sarma.

Integrated computational approaches for designing potent pyrimidine-based CDK9 inhibitors: 3D-QSAR, docking, and molecular dynamics simulations.

CDK9 is an emerging target for the development of anticancer drugs. The development of CDK9 inhibitors with significant potency had consistently posed a formidable challenge. In the current research, a number of computational methodologies, such as, 3D-QSAR, molecular docking, fingerprint analysis, molecular dynamic (MD) simulations followed by MMGB/PBSA and ADMET studies were used systemically to uncover the binding mechanism of pyrimidine derivatives against CDK9. The CoMFA and CoMSIA models having high q2 (0.53, 0.54) and r2 values (0.96, 0.93) respectively indicating that model could accurately predict the bioactivities of CDK9 inhibitors. Using the R-group exploration technique implemented by the Spark™ by Cresset group, the structural requirements revealed by the contour maps of model were utilized strategically to create an in-house library of 100 new CDK9 inhibitors. Additionally, the compounds from the in-house library were mapped into 3D-QSAR model which predicted pIC50 values comparable to the experimental values. A comparison between 3D-QSAR generated contours and molecular docking conformation of ligands was performed to elucidate the essentials of CDK9 inhibitor design. MD simulations (100 ns) were performed on the selected docked complexes A21, A14 and D98 which contributed in validating the binding interactions. According to the findings of binding free energy analysis (MMGB/PBSA), It was observed that residues CYS106 and GLU107 had a considerable tendency to facilitate ligand-protein interactions via H-bond interactions. The aforementioned findings have the potential to enhance researchers comprehension of the mechanism underlying CDK9 inhibition and may be utilized in the development of innovative and efficacious CDK9 inhibitors.

Molecular modeling of pyrrolo-pyrimidine based analogs as potential FGFR1 inhibitors: a scientific approach for therapeutic drugs.

Fibroblast growth factor receptors 1 (FGFR1) is an emerging target for the development of anticancer drugs. Uncontrolled expression of FGFR1 is strongly associated with a number of different types of cancers. Apart from a few FGFR inhibitors, the FGFR family members have not been thoroughly studied to produce clinically effective anticancer drugs. The application of proper computational techniques may aid in understanding the mechanism of protein-ligand complex formation, which may provide a better notion for developing potent FGFR1 inhibitors. In this study, a variety of computational techniques, including 3D-QSAR, flexible docking and MD simulation followed by MMGB/PBSA, H-bonds and distance analysis, have been performed to systematically explore the binding mechanism of pyrrolo-pyrimidine derivatives against FGFR1. The 3D-QSAR model was generated to deduce the structural determinants of FGFR1 inhibition. The high q2 and r2 values for the CoMFA and CoMSIA models indicated that the created 3D-QSAR models could reliably predict the bioactivities of FGFR1 inhibitors. The computed binding free energies (MMGB/PBSA) for the selected compounds were consistent with the ranking of their experimental binding affinities against FGFR1. Furthermore, per-residue energy decomposition analysis revealed that the residues Lys514 in catalytic region, Asn568, Glu571 in solvent accessible portion and Asp641 in DFG motif exhibited a strong tendency to mediate ligand-protein interactions through the hydrogen bonding and Van Der Waals interactions. These findings may benefit researchers in gaining better knowledge of FGFR1 inhibition and may serve as a guideline for the development of novel and highly effective FGFR1 inhibitors.Communicated by Ramaswamy H. Sarma.

Deep learning in drug discovery: a futuristic modality to materialize the large datasets for cheminformatics.

Artificial intelligence (AI) development imitates the workings of the human brain to comprehend modern problems. The traditional approaches such as high throughput screening (HTS) and combinatorial chemistry are lengthy and expensive to the pharmaceutical industry as they can only handle a smaller dataset. Deep learning (DL) is a sophisticated AI method that uses a thorough comprehension of particular systems. The pharmaceutical industry is now adopting DL techniques to enhance the research and development process. Multi-oriented algorithms play a crucial role in the processing of QSAR analysis, de novo drug design, ADME evaluation, physicochemical analysis, preclinical development, followed by clinical trial data precision. In this study, we investigated the performance of several algorithms, including deep neural networks (DNN), convolutional neural networks (CNN) and multi-task learning (MTL), with the aim of generating high-quality, interpretable big and diverse databases for drug design and development. Studies have demonstrated that CNN, recurrent neural network and deep belief network are compatible, accurate and effective for the molecular description of pharmacodynamic properties. In Covid-19, existing pharmacological compounds has also been repurposed using DL models. In the absence of the Covid-19 vaccine, remdesivir and oseltamivir have been widely employed to treat severe SARS-CoV-2 infections. In conclusion, the results indicate the potential benefits of employing the DL strategies in the drug discovery process.Communicated by Ramaswamy H. Sarma.

First Report of Fruit Rot Caused by Diaporthe amygdali on Papaya in Punjab, Pakistan.

Papaya (Carica papaya L.) is grown widely in tropical and sub-tropical regions (Ahmed et al. 2008). In Pakistan, papaya production and consumption are increasing due to its medicinal, nutritional, pharmacological properties and a rich source of antioxidant, vitamin B, potassium, and magnesium. In November 2021, 26 to 35% incidence of fruit rot was observed in 15 fields of Lahore, a district of Punjab, Pakistan. Affected fruit developed circular, gray-to-brown lesions (8 to 10 mm in diameter) with white mycelia forming on the surface of lesions. In advanced stages of the disease, the lesions enlarged in size and led to the rot of entire fruit. To isolate the causal agent, small tissue segments (1 to 2 cm) were excised from 15 symptomatic fruit, surface disinfected with 1% NaClO for 30 s, rinsed with sterile distilled water three times, air dried in laminar flow hood, aseptically transferred onto petri dishes containing potato dextrose agar (PDA) and incubated at 25℃ for 5 days with a 12-h photoperiod. Eleven isolates were obtained that produced white mycelia on PDA. Flask-shaped, dark-pigmented pycnidia formed on PDA after 18 days of incubation at 25°C, which produced α-conidia measuring 4.1 to 7.2 × 1.5 to 3.0 µm and ß-conidia measuring 16.4 to 25.5 × 1.0 to 1.6 µm (n = 40). α-conidia were hyaline, fusiform, and single-celled, whereas ß-conidia were one-celled, hyaline, and filiform. The morphological characteristics of the fungus were compatible with a Diaporthe species (Gomes et al. 2013). The internal transcribed spacer region (ITS) (OM865414 and OM865415), translation elongation factor 1-alpha (tef1) (OM831226 and OM831229), and histone H3 (HIS) (OM831227 and OM831228) of two representative isolates (UO02 and UO03) were amplified and sequenced using primers ITS1/ITS4 (White et al. 1990), EF1-728F/EF1-986R (Carbone and Kohn 1999), and CYLH3F/H3-1b (Chaisiri et al. 2021), respectively. Blast searches showed 99 to 100% nucleotide identity with reference sequences of several Diaporthe amygdali deposited in NCBI GenBank, including the ex-type strain CBS 126679. A pathogenicity test was also performed on harvested fruit of papaya cv. Bombay using isolates UO02 and UO03. Ten mature and healthy papaya fruit were surface disinfected with 1% NaClO solution for 1 min, rinsed with sterile water and dried. Each fruit was wounded twice with a sterile scalpel (4 to 5 mm incision on the peel) and a 5-mm agar disc with mycelia of each isolate was separately placed in each wound. The wounds were wrapped with Parafilm following inoculation. Sterile PDA plugs were used in separate inoculated controls. All wounds were sealed with parafilm. All fruit were maintained in plastic boxes at 25°C with 80% relative humidity. After 6 days of incubation, rot symptoms similar to those appearing on naturally-infected fruit were observed on inoculated fruits while controls remained asymptomatic. The experiment was repeated twice with similar findings. Diaporthe amygdali was re-isolated (100%) from inoculated fruit and the pathogen identification was confirmed by morphological and molecular analysis, thus fulfilling Koch's postulates. Previously, the pathogen has been reported as a causal agent of canker and shoot blight disease in other countries (Ko and Sun, 2003; Beluzan et al. 2021). To our knowledge, this is the first report of D. amygdali on papaya in Punjab Province of Pakistan. Papaya is an emerging fruit crop in Punjab Province and it is important to further investigate the presence of this pathogen in other papaya orchards of the province since D. amygdali may cause rapid disease outbreaks resulting in severe losses.

Zinc Essentiality, Toxicity, and Its Bacterial Bioremediation: A Comprehensive Insight.

Zinc (Zn) is one of the most abundantly found heavy metals in the Earth's crust and is reported to be an essential trace metal required for the growth of living beings, with it being a cofactor of major proteins, and mediating the regulation of several immunomodulatory functions. However, its essentiality also runs parallel to its toxicity, which is induced through various anthropogenic sources, constant exposure to polluted sites, and other natural phenomena. The bioavailability of Zn is attributable to various vegetables, beef, and dairy products, which are a good source of Zn for safe consumption by humans. However, conditions of Zn toxicity can also occur through the overdosage of Zn supplements, which is increasing at an alarming rate attributing to lack of awareness. Though Zn toxicity in humans is a treatable and non-life-threatening condition, several symptoms cause distress to human activities and lifestyle, including fever, breathing difficulty, nausea, chest pain, and cough. In the environment, Zn is generally found in soil and water bodies, where it is introduced through the action of weathering, and release of industrial effluents, respectively. Excessive levels of Zn in these sources can alter soil and aquatic microbial diversity, and can thus affect the bioavailability and absorption of other metals as well. Several Gram-positive and -negative species, such as Bacillus sp., Staphylococcus sp., Streptococcus sp., and Escherichia coli, Pseudomonas sp., Klebsiella sp., and Enterobacter sp., respectively, have been reported to be promising agents of Zn bioremediation. This review intends to present an overview of Zn and its properties, uses, bioavailability, toxicity, as well as the major mechanisms involved in its bioremediation from polluted soil and wastewaters.

Corrigendum: Zinc essentiality, toxicity, and its bacterial bioremediation: A comprehensive insight.

[This corrects the article DOI: 10.3389/fmicb.2022.900740.].

First Record of Chaetomium globosum Causing Leaf Spot of Pomegranate in Pakistan.

Pomegranate (Punica granatum L.) is a non-climacteric and a favorite fruit of tropical, sub-tropical and arid regions of the world. During a survey in autumn 2019, leaf lesions were observed on plants (cv. Kandhari) in different orchards of Muzaffargarh (30°4'27.7572″ N, 71°11'4.7544″ E), a major pomegranate-producing region in Punjab Province. Disease incidence ranged from 17 to 20%. Leaf lesions were initially small (1 to 3 mm in diameter), round, purple or reddish-brown, scattered spots. At later stages, spots increased in size and the centers of mature lesions became dark red or black with fungal sporulation. To isolate the pathogen, samples of leaf (5 × 5 mm) were cut from the junction of diseased and healthy tissue, surface disinfected in 75% alcohol for 30 s, sterilized with 6% sodium hypochlorite for 3 min, washed with sterile distilled water three times, air dried in laminar flow hood, and cultured on potato dextrose agar (PDA). After one week of incubation at 25 ± 2°C with a 12-h photoperiod, fungal colonies developed, which were initially white and became pale yellow with olivaceous green mycelium after 20 days. On PDA, ascomata were olivaceous green, with a papillate ostiole, globose or ovoidal to obovoidal (155 to 220 × 120 to 240 µm, n=50). Terminal and lateral setae were abundant, brown, and tapering toward the tips (4 to 6 µm, n=50). Asci were greenish and lemon-shaped (6 to 8 × 9 to 13.5 µm, n=50). Ascospores were limoniform and olivaceous gray-brown (10 to 11.5 × 7 to 9 µm, n=50). These morphological characteristics were consistent with the morphology of Chaetomium globosum (Lan et al. 2011; Wang et al. 2016). Genomic DNA was extracted from two isolates and identification of the pathogen was confirmed by amplification and sequencing of the internal transcribed spacer region (ITS) and the partial translation elongation factor 1-α (TEF1) gene using ITS1/ITS4 (White et al. 1999) and EF1-983F/EF1-2218R primers (Wang et al. 2016), respectively. The sequences of the PCR products were deposited in GenBank with accession numbers MW522514, MW522352 (ITS), and MW530423, MW530424 (TEF1). BLAST results of the obtained sequences of the ITS and TEF1 genes revealed 100% (513/513 bp) and 99.78% (927/929 bp) similarity with those of C. globosum in GenBank (ITS: KX834823 and KT898637, and TEF1: MG812564 and KC485028). To confirm pathogenicity, inoculum was prepared by harvesting conidia from 10-day-old culture grown in PDA. The surface-disinfected (70% ethyl alcohol, 30 s) leaves of ten 1-year-old seedlings (cv. Kandhari) were sprayed with a spore suspension (1×106 conidia/ml). Leaves of ten seedlings sprayed with sterile distilled water served as controls. All seedlings were covered with plastic bags and placed in a greenhouse at 26°C with 12 h photoperiod. After eight days, symptoms on inoculated leaves were similar to those observed in the orchards; no symptoms were observed on controls. The fungus was reisolated from all symptomatic tissues. C. globosum has been reported on Punica granatum (Guo et al. 2015), Cannabis sativa (Chaffin et al. 2020) and Brassica oleracea (Zhu et al. 2020). This is the first report of C. globosum causing leaf spot on pomegranate in Pakistan. This finding suggests a potential threat to pomegranate production in Pakistan and further studies should focus on effective prevention and control practices of this disease.

Phytochemical profiling, antioxidant and antiproliferation potential of Euphorbia milii var.: Experimental analysis and in-silico validation.

This study was aimed to investigate the anticancer potential of Euphorbia milii (E. milii) using an exquisite combination of phytopharmacological and advanced computational techniques. The chloroform fraction (Em-C) of E. milii methanol extract showed the highest antioxidant activity (IC50: 6.41 ± 0.99 µg/ml) among all studied fractions. Likewise, Em-C also showed significant cytotoxicity (IC50: 11.2 ± 0.8 µg/ml) when compared with that of standard compound 5-fluorouracil (5-FU) (IC50: 4.22 ± 0.6 µg/ml) against hepatocarcinoma cell line (HepG2). However, in a human cervical cancer cell line (HeLa), Em-C demonstrated a non-significant difference in cytotoxicity (22.1 ± 0.8 µg/ml) when compared with that of 5-FU (IC50: 6.87 ± 0.5 µg/ml). Furthermore, Western blot and qRT-PCR analysis revealed that the suppression of HepG2 cells was the consequence of a tremendous decrease in CDK2 and E2F1 protein expression. The GC-MS analysis of Em-C revealed the unique presence of cyclobarbital (CBT) and benzodioxole derivative (BAN) as major constituents. Furthermore, molecular docking of compounds BAN, CBT, and MBT into the binding site of different molecular targets i.e. cyclin dependent kinase 2 (CDK2), thymidylate synthase (TS), caspase 3, BCL2 and topoisomerase II was carried out. Compounds BAN and CBT have demonstrated remarkable binding affinity towards CDK2 and thymidylate synthase, respectively. Molecular dynamic simulation studies have further confirmed the finding of docking analysis, suggesting that CDK2 and TS can act as an attractive molecular target for BAN and CBT, respectively. It can be concluded that these E. milii phytoconstituents (BAN and CBT) may likely be responsible for anti-invasive activity against HepG2 cells.

Repellency, Toxicity, Gene Expression Profiling and In Silico Studies to Explore Insecticidal Potential of Melaleuca alternifolia Essential Oil against Myzus persicae.

In the current study, deterrent assay, contact bioassay, lethal concentration (LC) analysis and gene expression analysis were performed to reveal the repellent or insecticidal potential of M. alternifolia oil against M. persicae. M. alternifolia oil demonstrated an excellent deterrence index (0.8) at 2 g/L after 48 h. The oil demonstrated a pronounced contact mortality rate (72%) at a dose of 4 g/L after 24 h. Probit analysis was performed to estimate LC-values of M. alternifolia oil (40%) against M. persicae (LC30 = 0.115 g/L and LC50 = 0.37 g/L respectively) after 24 h. Furthermore, to probe changes in gene expression due to M. alternifolia oil contact in M. persicae, the expression of HSP 60, FPPS I, OSD, TOL and ANT genes were examined at doses of LC30 and LC50. Four out of the five selected genes-OSD, ANT, HSP 60 and FPPS I-showed upregulation at LC50, whereas, TOL gene showed maximum upregulation expression at LC30. Finally, the major components of M. alternifolia oil (terpinen-4-ol) were docked and MD simulated into the related proteins of the selected genes to explore ligand⁻protein modes of interactions and changes in gene expression. The results show that M. alternifolia oil has remarkable insecticidal and deterrent effects and also has the ability to affect the reproduction and development in M. persicae by binding to proteins.