MD Simulation Studies for Selective Phytochemicals as Potential Inhibitors against Major Biological Targets of Diabetic Nephropathy.

Diabetes is emerging as an epidemic and is becoming a public health concern worldwide. Diabetic nephropathy is one of the serious complications of diabetes, and about 40% of individuals with diabetes develop diabetic nephropathy. The consistent feature of diabetes and its associated nephropathy is hyperglycemia, and in some cases, hyperamylinemia. Currently, the treatment includes the use of medication for blood pressure control, sugar control, and cholesterol control, and in the later stage requires dialysis and kidney transplantation, making the management of this complication very difficult. Bioactive compounds, herbal medicines, and extracts are extensively used in the treatment and prevention of several diseases, and some are reported to be efficacious in diabetes too. Therefore, in this study, we tried to identify the therapeutic potential of phytochemicals used in in silico docking and molecular dynamic simulation studies using a library of 5284 phytochemicals against the two potential targets of type 2 diabetes-associated nephropathy. We identified two phytochemicals (i.e., gentisic acid and michelalbine) that target human amylin peptide and dipeptidyl peptidase-4, respectively, with good binding affinity. These phytochemicals can be further evaluated using in vitro and in vivo studies for their anti-hyperglycemia and anti-hyperamylinemia effects.

Molecular cloning, expression, purification, and functional characterization of SP-22 gene from Bombyx mori.

Serine protease (SPs) is one of the immune enzyme's molecules that play a main role in the variation of a physiological process by controlling protease actions in vertebrates. For example, signaling cells, protector and improvement, which are included in melanization, are utilized to cascade with the meddling pathogens and defense the harmed tissue in insects. In this study, we explore the biochemical process of (SP-22) from Bombyx mori. Reverse-transcription polymerase chain reaction (RT-PCR) discloses that BmSP-22 is expressed in all tissues including the fat body. The formative expression profile of BmSP-22 reveal that BmSP-22 messenger RNA is expressed constitutively in larvae. Injection of recombinant BmSP-22 into B. mori larvae reduces significantly the transcript levels of antimicrobial peptides in the fat body. Our results suggest that BmSP-22 plays an important role in the innate immunity of B. mori and possibly in other insects.

Molecular dynamic analyses of the interaction of SARS-CoV-1 or 2 variants with various angiotensin-converting enzyme-2 species.

The transmembrane glycoprotein angiotensin-converting enzyme 2 (ACE2) is a key component of the renin-angiotensin system (RAS). It was shown to be the receptor of severe acute respiratory syndrome coronavirus 2 in the COVID-19 outbreak (SARS-COV-2). Furthermore, ACE2 aids in the transport of amino acids across the membrane. ACE2 is lost from the membrane, resulting in soluble ACE2 (sACE2). We aim to examine the structural conformation alterations between SARS-CoV-1 or 2 variants at various periods with ACE2 from various sources, particularly in the area where it interacts with the viral protein and the receptor. It is important to study the molecular dynamics of ACE2/SARS-COV RBD when the structure is available on the database. Here we analyzed the crystal structure of ACE2 from Human, Dog, Mus, Cat, and Bat ACE2 in complex with RBD from SARS-COV-1 and SARS-COV-2. The result shows, there is a variation in the type of residues, number of contact atoms and hydrogen bonds in ACE2 and RBD during the interaction interfaces. By using molecular dynamics simulation, we can measure RMSD, RMSF, SASA, Rg and the difference in the percentage of α helix and ß strand. As bat ACE2 & SARS-CoV-2 RBD found to have a high amount of ß strand compared to another structure complex, while hACE2 & SARS-CoV-1 RBD has fewer amounts of ß strand. Our study provides a deep view of the structure which is available and a summary of many works around ACE2/SARS-CoV RBD interaction.Communicated by Ramaswamy H. Sarma.

Anticancer, antioxidant activities and molecular docking study of thiazolidine-4-one and thiadiazol derivatives.

Liver cancer accounts for a major portion of the global cancer burden. In many nations, the prevalence of this condition has risen in recent decades. New series of thiazolidinones and thiadiazolidine have been designed, synthesized, and evaluated for potential antioxidant and antihepatocarcinogenic activity. The antioxidant activity was evaluated using a DPPH assay. Furthermore, we examined the compounds against Hepg-2 cells using MTT assay, flow cytometry analysis through the cell cycle, reactive oxygen species, and apoptosis. The result showed that compound 6b has the highest antioxidant activity with IC50 = 60.614 ± 0.739 µM. The anticancer activity showed that compounds 5 and 6b have significant toxicity against liver cancer cells Hepg2, IC50 values (9.082 and 4.712) µM, respectively. Flow cytometry experiments revealed that compound 5 arrested Hepg-2 cells in the S process, while compound 6b arrested Hepg-2 cells in the G1. Compound 6b had a greater reduction in reactive oxygen species and late apoptosis than compound 5. Substantially, compound 5 had affinity energies of -7.6 and -8.5 for Akt and CDK4 proteins, respectively, but compound 6b had affinity energies of -7.8 and -10.1 for Akt1 and CDK4 proteins, respectively. Consequently, compound 6b had lower binding energies than compound 5. In this work, we used multiple bioinformatics methods to shed light on the prospective therapeutic use of these series as novel candidates to target immune cells in the tumor microenvironment of hepatocellular carcinomas such as CD8+ T cells, endothelial cells, and hematopoietic stem cells.

Study on Molecular Anti-tumor Mechanism of 2-Thiohydantoin Derivative based on Molecular Docking and Bioinformatic Analyses.

OBJECTIVE: Several methods for synthesizing 2-thiohydantoin derivatives have been devised and exploited, and they have found widespread application as antioxidants, antimicrobials, antivirals, and anticancer agents. As a result, we tried to understand the underlying processes of the 2- thiohydantoin derivative's anti-LIHC activity. METHODS: We predicted the anticancer mechanism of N-(4-oxo-5-(2-oxo-2-(p-tolylamino)ethyl)-3- phenyl-2-thioxoimidazolidin-1-yl)benzamide as a derivative of 2-thiohydantoin by utilizing molecular docking and molecular dynamic simulation. Furthermore, based on the results of molecular dynamic modelling, we employed bioinformatics to anticipate the immunotherapy of this molecule in the tumor microenvironment (TME) of Liver Hepatocellular Carcinoma (LIHC) patients. Next, we examined how this derivative affected proliferation, cell cycle progression, reactive oxygen species production, and apoptosis in HepG2 cancer cells. RESULTS: Substantially, our investigation revealed that the IC50 value was 2.448 µM and that it arrested the cell cycle of HepG2 in the S phase. Furthermore, molecular docking and dynamics studies revealed a worthy interaction of this compound with AKT1 and CDK2 proteins. Considerably, AKT1 and CDK2 have negative affinity energies of -10.4 kcal/mol and -9.6 kcal/mol, respectively. Several bioinformatic tools were used in this investigation to provide insight into the future clinical application of this derivative as a novel candidate to target immune cells such as macrophages, neutrophils, eosinophils, and CD8+ T cells. CONCLUSION: The relevance of this 2-thiohydantoin derivative was demonstrated by our experimental tests, docking studies, and bioinformatics analysis, and it may be investigated as a lead molecule for anticancer medicines, notably as AKT1 and CKD2 inhibitors.

Dual synergistic inhibition of COX and LOX by potential chemicals from Indian daily spices investigated through detailed computational studies.

Cyclooxygenase (COX) and Lipoxygenase (LOX) are essential enzymes for arachidonic acid (AA) to eicosanoids conversion. These AA-derived eicosanoids are essential for initiating immunological responses, causing inflammation, and resolving inflammation. Dual COX/5-LOX inhibitors are believed to be promising novel anti-inflammatory agents. They inhibit the synthesis of prostaglandins (PGs) and leukotrienes (LTs), but have no effect on lipoxin formation. This mechanism of combined inhibition circumvents certain limitations for selective COX-2 inhibitors and spares the gastrointestinal mucosa. Natural products, i.e. spice chemicals and herbs, offer an excellent opportunity for drug discovery. They have proven anti-inflammatory properties. However, the potential of a molecule to be a lead/ drug candidate can be much more enhanced if it has the property of inhibition in a dual mechanism. Synergistic activity is always a better option than the molecule's normal biological activity. Herein, we have explored the dual COX/5-LOX inhibition property of the three major potent phytoconsituents (curcumin, capsaicin, and gingerol) from Indian spices using in silico tools and biophysical techniques in a quest to identify their probable inhibitory role as anti-inflammatory agents. Results revealed the dual COX/5-LOX inhibitory potential of curcumin. Gingerol and capsaicin also revealed favorable results as dual COX/5-LOX inhibitors. Our results are substantiated by target similarity studies, molecular docking, molecular dynamics, energy calculations, DFT, and QSAR studies. In experimental inhibitory (in vitro) studies, curcumin exhibited the best dual inhibitory activities against COX-1/2 and 5-LOX enzymes. Capsaicin and gingerol also showed inhibitory potential against both COX and LOX enzymes. In view of the anti-inflammatory potential these spice chemicals, this research could pave the way for more scientific exploration in this area for drug discovery.

Metformin as a promising target for DPP4 expression: computational modeling and experimental validation.

Metformin is a regularly prescribed and low-cost generic medication. Metformin has been proposed as a target for Dipeptidyl-peptidase 4 (DPP4) expression in various clinical disorders. We provide insilco investigations on molecular docking and dynamic modeling of metformin and DPP4 potential interactions. Moreover, we conducted bioinformatic studies to highlight the clinical significance of DPP4 expression and mutation in various types of malignancies, as well as the invasion of different immune cells into the tumor microenvironment. We believe the present proposal's findings have crucial implications for understanding how metformin may confer health advantages by targeting DPP4 expression in malignancies.

Molecular dynamic and bioinformatic studies of metformin-induced ACE2 phosphorylation in the presence of different SARS-CoV-2 S protein mutations.

The SARS-CoV-2 infection activates host kinases and causes high phosphorylation in both the host and the virus. There were around 70 phosphorylation sites found in SARS-CoV-2 viral proteins. Besides, almost 15,000 host phosphorylation sites were found in SARS-CoV-2-infected cells. COVID-19 is thought to enter cells via the well-known receptor Angiotensin-Converting Enzyme 2 (ACE2) and the serine protease TMPRSS2. Substantially, the COVID-19 infection doesn't induce phosphorylation of the ACE2 receptor at Serin-680(s680). Metformin's numerous pleiotropic properties and extensive use in medicine including COVID-19, have inspired experts to call it the "aspirin of the twenty-first century". Metformin's impact on COVID-19 has been verified in clinical investigations via ACE2 receptor phosphorylation at s680. In the infection of COVID-19, sodium-dependent transporters including the major neutral amino acid (B0AT1) is regulated by ACE2. The structure of B0AT1 complexing with the COVID-19 receptor ACE2 enabled significant progress in the creation of mRNA vaccines. We aimed to study the impact of the interaction of the phosphorylation form of ACE2-s680 with wild-type (WT) and different mutations of SARS-CoV-2 infection such as delta, omicron, and gamma (γ) on their entrance of host cells as well as the regulation of B0AT1by the SARS-CoV-2 receptor ACE2. Interestingly, compared to WT SARS-CoV-2, ACE2 receptor phosphorylation at s680 produces conformational alterations in all types of SARS-CoV-2. Furthermore, our results showed for the first time that this phosphorylation significantly influences ACE2 sites K625, K676, and R678, which are key mediators for ACE2-B0AT1 complex.

Novel slow-binding reversible acetylcholinesterase inhibitors based on uracil moieties for possible treatment of myasthenia gravis and protection from organophosphate poisoning.

A series of new compounds in which uracil and 3,6-dimethyluracil moieties are bridged with different spacers were prepared and evaluated in vitro for the acetyl- and butyrylcholinesterase (AChE and BChE) inhibitory activities. These bisuracils are shown to be very effective inhibitors of AChE, inhibiting the enzyme at nano- and lower molar concentrations with extremely high selectivity for AChE vs. BChE. Kinetic analysis showed that the lead compound 2h acts as a slow-binding inhibitor of AChE and possess a long drug-target residence time (τ = 1/koff = 18.6 ± 7.5 min). Moreover, compound 2h ameliorated muscle weakness in myasthenia gravis rat model with a lower effective dose and longer lasting effect than pyridostigmine bromide. Besides, it was shown that compound 2h has an effect of increasing efficiency of antidotal therapy as a pretreatment for poisoning by organophosphates.

Revisiting macrophages in ovarian cancer microenvironment: development, function and interaction.

Tumor-associated macrophages (TAMs) are an important component of the tumor microenvironment (TME) and have been linked to immunosuppression and poor prognosis. TAMs have been shown to be harmful in ovarian cancer (OC), with a positive correlation between their high levels of tumors and poor overall patient survival. These cells are crucial in the progression and chemoresistance of OC. The primary pro-tumoral role of TAMs is the release of cytokines, chemokines, enzymes, and exosomes that directly enhance the invasion potential and chemoresistance of OC by activating their pro-survival signalling pathways. TAMs play a crucial role in the metastasis of OC in the peritoneum and ascities by assisting in spheroid formation and cancer cell adhesion to the metastatic regions. Furthermore, TAMs interact with tumor protein p53 (TP53), exosomes, and other immune cells, such as stem cells and cancer-associated fibroblasts (CAFs) to support the progression and metastasis of OC. In this review we revisit development, functions and interactions of TAMs in the TME of OC patients to highlight and shed light on challenges and excitement down the road.

GATA3 as an immunomodulator in obesity-related metabolic dysfunction associated with fatty liver disease, insulin resistance, and type 2 diabetes.

Obesity is the leading risk factor associated with Metabolic dysfunction Associated with Fatty Liver Disease (MAFLD), Insulin Resistance (IR), and type 2 diabetes (T2DM). Notably, MAFLD affects 25% of the world's adult population, ranging from 13.5% in Africa to 31.8% in the Middle East. The prevalence of MAFLD is 80-90% in obese adults and 30-50% in patients with diabetes. According to the recent WHO update, more than 400 million people will experience T2DM by 2025. Furthermore, the worldwide obesity incidence rate has risen in the preceding years. Adipogenesis deterioration is a critical step in the induction of obesity correlated with MAFLD, IR and T2DM. The well-known transcription factor GATA3 is highly expressed in the preadipocytes-adipocytes transition of embryonic stem cells and obese people with IR. In this regard, the reduction of GATA3 improves the differentiation of adipocytes. Omental adipose tissue inflammation by upregulation of macrophages infiltration is strongly linked with body mass index in insulin tolerance of obese people. In particular, the dynamic interaction between macrophages and adipocytes significantly regulates obese adipose tissue's inflammatory status and influences IR by reducing the differentiation of adipocytes, macrophage function, and glucose transport. Emerging evidence demonstrated that GATA3 is a master regulator for macrophage polarization and infiltration. Hence, we will shed light on GATA3 as an emerging target for immunomodulation in human obesity associated with MAFLD, IR, and T2DM by reducing macrophages' recruitment and inflammation of muscles and liver.

Molecular dynamic study of SARS-CoV-2 with various S protein mutations and their effect on thermodynamic properties.

Studying the structure of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein is important to understand the infection process. The S protein is necessary in completing the virus life cycle and is responsible for the appearance of new variants and drug and vaccine resistance. Understanding the structure and dynamics of biological macromolecules is essential for understanding how they function. In this work, we investigated the effects of mutations on S protein stability and solubility through molecular dynamic (MD) simulation in a 100 ns (ns) period. We screened four variants in addition to the wild type (WT). Results show that changes on MD simulation parameters of S protein indicate fluctuations and changes in the conformation, especially in the area between 300 and 600 amino acids (aa). This provides us an image of how the virus protein can reshape itself to adapt to any changes that occur in human angiotensin-converting enzyme 2 or drugs that can target the protein region. Our results also show that the Brazil variant has high fluctuations and unstable folding at some stages compared with other variants.

Botrytis cinerea alcohol dehydrogenase mediates fungal development, environmental adaptation and pathogenicity.

Botrytis cinerea is an economically critical necrotrophic fungus that infecting many types of plants species. Although the lifestyle adaptations and genetic foundations of several enzymes and metabolites involved in B. cinerea virulence during host plant infection are well studied, the role of B. cinerea alcohol dehydrogenase (ADH) enzymes in these processes is poorly understood. Herein, we identified a significant up-regulation of the transcriptional levels of the BcADH1 gene during the tomato - B. cinerea strain B0510 interaction and at the early stage of infection. Substantially, we used a recent approach for replacement of gene by utilizing homologous recombination to generate knock-out mutants (Δbcadh1) and their effective complementary strains (Δbcadh1/C). A strong difference in the morphology of Δbcadh1 mutants from the wild type (WT) was detected, with respect to the conidiospore, conidial germination, and formation of branches, sporulation and sclerotia. In addition, the Δbcadh1 mutants showed significant differences in their virulence on tomato leaves relative to the WT. Moreover, the Δbcadh1 mutants appeared to have higher sensitivity to oxygen limitation (hypoxia) and reactive oxygen species, and had lost their ability of alcoholic fermentation compared with the WT and complementary strains. These results provide strong evidence for the requirement of the ADH1 gene for fungal development, environmental adaptation and its ability for full pathogenicity.Communicated by Ramaswamy H. Sarma.

In the face of the future, what do we learn from COVID-19?

Coronavirus disease (COVID-19) is a highly contagious infection caused by a recently identified coronavirus. The first known case was discovered in December 2019 in Wuhan, China. Since then, the illness has spread globally, resulting in an ongoing epidemic. Here, we would like to address one of the most pressing and outstanding questions which rise about COVID-19 during the year and a half since its discovery: what have we learned from COVID-19?

Repurposing benzimidazole and benzothiazole derivatives as potential inhibitors of SARS-CoV-2: DFT, QSAR, molecular docking, molecular dynamics simulation, and in-silico pharmacokinetic and toxicity studies.

Density Functional Theory (DFT) and Quantitative Structure-Activity Relationship (QSAR) studies were performed on four benzimidazoles (compounds 1-4) and two benzothiazoles (compounds 5 and 6), previously synthesized by our group. The compounds were also investigated for their binding affinity and interactions with the SARS-CoV-2 Mpro (PDB ID: 6LU7) and the human angiotensin-converting enzyme 2 (ACE2) receptor (PDB ID: 6 M18) using a molecular docking approach. Compounds 1, 2, and 3 were found to bind with equal affinity to both targets. Compound 1 showed the highest predictive docking scores, and was further subjected to molecular dynamics (MD) simulation to explain protein stability, ligand properties, and protein-ligand interactions. All compounds were assessed for their structural, physico-chemical, pharmacokinetic, and toxicological properties. Our results suggest that the investigated compounds are potential new drug leads to target SARS-CoV-2.