Targeting an Old Foe for Cancer: A Molecular Dynamics Perspective to Unravel the Specific Binding Nature of 2-Methoxy Estradiol to Human ß-Tubulin Isotypes.

Microtubules, composed of α- and ß-tubulin subunits are crucial for cell division with their dynamic tissue-specificity which is dictated by expression of isotypes. These isotypes differ in carboxy-terminal tails (CTTs), rich in negatively charged acidic residues in addition to the differences in the composition of active site residues. 2-Methoxy estradiol (2-ME) is the first antimicrotubule agent that showed less affinity toward hemopoietic-specific ß1 isotype consequently preventing myelosuppression toxicity. The present study focuses on the MD-directed conformational analysis of 2-ME and estimation of its binding affinity in the colchicine binding pocket of various ß-tubulin isotypes combined with the α-tubulin isotype, α1B. AlphaFold 2.0 was used to predict the 3D structure of phylogenetically divergent human ß-tubulin isotypes in dimer form with α1B. The dimeric complexes were subjected to induced-fit docking with 2-ME. The statistical analysis of docking showed differences in the binding characteristics of 2-ME with different isotypes. The replicas of atom-based molecular dynamic simulations of the best conformation of 2-ME provided insights into the molecular-level details of its binding pattern across the isotypes. Furthermore, the MM/GBSA analyses revealed the specific binding energy profile of 2-ME in ß-tubulin isotypes. It also highlighed, 2-ME exhibits the lowest binding affinity toward the ß1 isotype as supported by experimental study. The present study may offer useful information for designing next-generation antimicrotubule agents that are more specific and less toxic.

De novo design of potential peptide analogs against the main protease of Omicron variant using in silico studies.

SARS-CoV-2 and its variants are crossing the immunity barrier induced through vaccination. Recent Omicron sub-variants are highly transmissible and have a low mortality rate. Despite the low severity of Omicron variants, these new variants are known to cause acute post-infectious syndromes. Nowadays, novel strategies to develop new potential inhibitors for SARS-CoV-2 and other Omicron variants have gained prominence. For viral replication and survival the main protease of SARS-CoV-2 plays a vital role. Peptide-like inhibitors that mimic the substrate peptide have already proved to be effective in inhibiting the Mpro of SARS-CoV-2 variants. Our systematic canonical amino acid point mutation analysis on the native peptide has revealed various ways to improve the native peptide of the main protease. Multi mutation analysis has led us to identify and design potent peptide-analog inhibitors that act against the Mpro of the Omicron sub-variants. Our in-depth analysis of all-atom molecular dynamics studies has paved the way to characterize the atomistic behavior of Mpro in Omicron variants. Our goal is to develop potent peptide-analogs that could be therapeutically effective against Omicron and its sub-variants.

An in silico study of protein-protein interactions and design of novel peptides for TrkA in ameloblastoma.

Ameloblastoma is a benign odontogenic jawbone tumor. The binding of Nerve growth factor (NGF) to receptor tyrosine kinase A (TrkA) promotes cell survival, proliferation, and differentiation via PI3K/AKT and Ras/MAPK signaling. Although the exact cause of ameloblastoma remains unknown, elevated levels of NGF and TrkA expression in ameloblastoma are associated with aggressive tumor behavior and poor patient outcomes. It is previously demonstrated that His 4, Arg 9, and Glu 11 residues of NGF made crucial interactions with the TrkA subunit. The main aim of our present study to develop potential therapeutic strategies by identifying promising peptide candidates. The objectives include starting with a detailed in silico analysis to identify a crucial peptide sequence of NGF that is bound by TrkA, creating a library of novel peptides from the identified peptide sequence through a single-point mutation on interacting residues (His 4, Arg 9, and Glu 11), and selecting the top peptides based on docking score, interactions analysis, and desirable pose analysis. The study ultimately designed a hybrid peptide candidate through the simultaneous and continuous mutation of the top residues, resulting in a peptide that exhibited a more specific interaction with TrkA, blocking the binding site and preventing the interaction between NGF and TrkA.Communicated by Ramaswamy H. Sarma.

Emerging Therapies and Therapeutic Targets for Composite Liver Disease: NASH.

BACKGROUND: Liver diseases continue to destroy the lives of people, one of which is known as Non-alcoholic Steatohepatitis (NASH) that becomes a serious liver disease all around the world over the last few years. Non-alcoholic Steatohepatitis (NASH) is a progressive form of Nonalcoholic Fatty Liver Disease (NAFLD) and is characterized by liver steatosis, inflammation, different degrees of fibrosis, and hepatocellular injury. The inflammatory mediators play a vital role in the transition of Non-alcoholic Fatty Liver (NAFL) to Non-alcoholic Steatohepatitis (NASH), which further leads to Hepatocellular Carcinoma (HCC) and becomes a cause of liver transplantation. OBJECTIVES: Considering the severity and complexity of the disease, we aim to summarize the works of various research groups that are working in the area of NASH to find a sophisticated treatment. RESULTS: The present review focused on various factors that are responsible for the development and progression of this prevalent disease, emerging pharmacotherapies as well as therapeutic targets that have been utilized for the treatment of NASH. We also have conducted the structural analysis of available targets, which will be helpful for the enhancement of drug discovery through the implementation of in silico methods. CONCLUSION: Efforts have been made to provide an update on research in the area of NASH, including the pharmacological agents that are currently undergoing clinical trials for the treatment of NASH. Besides the massive research, still, gaps and challenges are there in the drug development for NASH that also have been discussed.

Bifunctional robots inducing targeted protein degradation.

The gaining importance of Targeted Protein Degradation (TPD) and PROTACs (PROteolysis-TArgeting Chimeras) have drawn the scientific community's attention. PROTACs are considered bifunctional robots owing to their avidity for the protein of interest (POI) and E3-ligase, which induce the ubiquitination of POI. These molecules are based on event-driven pharmacology and are applicable in different conditions such as oncology, antiviral, neurodegenerative disease, acne etc., offering tremendous scope to researchers. In this review, primarily, we attempted to compile the recent works available in the literature on PROTACs for various targeted proteins. We summarized the design and development strategies with a focus on molecular information of protein residues and linker design. Rationalization of the ternary complex formation using Artificial Intelligence including machine & deep learning models and traditionally followed computational tools are also included in this study. Moreover, details describing the optimization of PROTACs chemistry and pharmacokinetic properties are added. Advanced PROTAC designs and targeting complex proteins, is summed up to cover the wide spectrum.

Peripheral neuropathy induced by red yeast rice in a patient with a known small bowel gastrointestinal tumour.

Peripheral neuropathy is a well-recognised side effect of the cholesterol-lowering statins. Red yeast rice (RYR) is a traditional Chinese herb, widely available over-the-counter that has also been found to reduce cholesterol. Little data is available regarding its side effect profile. We report a case of a 60-year-old male receiving therapeutic imatinib for metastatic gastrointestinal tumour (GIST), who developed peripheral neuropathy while also taking RYR. The symptoms completely settled following withdrawal of the RYR and he has subsequently continued to take imatinib for over 2 years with no adverse effects. Further research into the safety profile of RYR is needed. The importance of questioning patients about over the counter medications and herbal remedies cannot be overemphasised.