Computational insights into KRAS G12C inhibition: exploring possible repurposing of Azacitidine and Ribavirin

Kirsten rat sarcoma (KRAS) stands out as the most prevalent mutated oncogene, playing a crucial role in the initiation and progression of various cancer types, including colorectal, lung and pancreatic cancer. The oncogenic modifications of KRAS are intricately linked to tumor development and are identified in 22% of cancer patients. This has spurred the necessity to explore inhibition mechanisms, with the aim of investigating and repurposing existing drugs for diagnosing cancers dependent on KRAS G12C In this investigation, 26 nucleoside-based drugs were collected from literature to assess their effectiveness against KRAS G12C. The study incorporates in-silico molecular simulations and molecular docking examinations of these nucleoside-derived drugs with the KRAS G12C protein using Protein Data Bank (PDB) ID: 5V71. The docking outcomes indicated that two drugs, Azacitidine and Ribavirin, exhibited substantial binding affinities of -8.7 and -8.3 kcal/mol, respectively. These drugs demonstrated stability in binding to the active site of the protein during simulation studies. Root mean square deviation (RMSD) analyses indicated that the complexes closely adhered to an equilibrium RMSD value ranging from 0.17 to 0.2 nm. Additionally, % occupancies, bond angles and the length of hydrogen bonds were calculated. These findings suggest that Azacitidine and Ribavirin may potentially serve as candidates for repurposing in individuals with KRAS-dependent cancers.Communicated by Ramaswamy H. Sarma.

In-vivo anti-epileptic study of newly synthesized pregabalin derivatives based on docking studies

OBJECTIVE

The goal of the present study is to examine pretreatment with Schiff bases and derivatives of pregabalin along with their metal (Zn and Cu) complexes on the severity of epilepsy, latency time, duration of convulsions, seizure score and survival rate in mice.

METHODS

To achieve the goal, a molecular docking study of analogues was carried out on a specific molecular target, such as the alpha-2δ receptor (PDB ID: 6ND9); which revealed the significant binding affinity of the analogs to their respective target. Based on the docking information, all pregabalin derivatives were synthesized and in-vivo antiepileptic effect was confirmed by applying the PTZ model that prioritized the most crucial significant points responsible for biological activity.

RESULTS

The test compounds markedly increased the latency of the first seizure and reduced the frequency of seizures throughout the body and frequent spinning and jumps. Additionally, treatment with pregabalin derivatives in mice that received PTZ significantly reduced the duration of seizures and seizure score. However, it increased the survival rate of the mice.

DISCUSSION

Since the newly synthesized compounds were more active as compared to the parent drug in some respects; therefore, the expansion of the project can be planned to explore clinical side of the drugs in the future.

Exploring the potential of propanamide-sulfonamide based drug conjugates as dual inhibitors of urease and cyclooxygenase-2: biological and their in silico studies

Derivative synthesis has been a crucial method for altering the effects of already-approved medications, especially to lessen adverse effects and enhance results. Making use of this multi-target approach, a series of naproxen-sulfa drug conjugates was designed and synthesized. The newly designed conjugates were confirmed by spectroscopic techniques like IR, 1HNMR, 13CNMR, and elemental analysis. The conjugates were screened for anti-inflammatory, urease, and cyclooxygenase-2 (COX-2) inhibition. Naproxen conjugated with sulfanilamide, sulfathiazole, and sulfaguanidine was found potent and showed a competitive mode of urease inhibition, with IC50 (µM) values 6.69 ± 0.11, 5.82 ± 0.28, 5.06 ± 0.29, respectively. When compared to other screened conjugates, the naproxen-sulfamethoxazole conjugation showed better anti-inflammatory action by inhibiting induced edema by 82.8%, which is comparable to the medication indomethacin (86.8% inhibition). Whereas it exhibited 75.4% inhibition of COX-2 at 10 µM concentration which is comparable with the reference drug (celecoxib, 77.1% inhibition). Moreover, the binding modes of competitive inhibitors with the urease and COX-2 receptor were predicted through molecular docking studies and their stability analysis through MD simulations showed that these compounds made stable complexes with the respective targets and there were no conformational changes that occurred during simulation. The obtained results showed that the conjugates of approved therapeutic molecules may lead to the development of novel types of pharmacological agents in the treatment of several pathological disorders where urease and COX-2 enzymes are involved.

Design, synthesis, in vitro and in silico bioactivity profiles of new urea/thiourea derivatives of 2-pyridyl piperazine as potent antioxidant and antimicrobial agents: chemo-bio-computational approach

Synthesis of a series of new urea and thiourea derivatives of 2-pyridyl piperazine was accomplished by reacting various isocyanates and isothiocyanates in the presence of triethylamine (TEA) at 50 °C. All the title compounds were obtained in high yields and their structures were characterized by IR, ¹H, ¹³C NMR, Mass spectral, and Elemental analysis. The synthesized compounds were screened for in vitro and in silico antioxidant and antimicrobial activities. All the title compounds exhibited potent antioxidant and antimicrobial activities. Out of all, 2c and 2f against DPPH, H₂O₂ and Nitro oxide have exhibited significant activity and the levels of activity were higher than the reference compounds, ascorbic acid and BHT. Whereas 2a, 2c, 2f and 2j have shown prominent activity in terms of zone of inhibition against all the microbial strains tested than the standards such as levofloxacin and nystatin. In addition in silico studies also conveyed the same that is 2a, 2c, 2f and 2j have displayed the highest binding energies against peroxiredoxins and DNA gyrase protein than the standards akin to the rest of the compounds. In overall, 2c and 2f have exhibited most promising antioxidant and antimicrobial activity than the rest of the title compounds in vitro and in silico. Hence, 2c and 2f will stand as a lead and promising antioxidant and antimicrobial drug candidates in future.

Amino acid conjugates of 2-mercaptobenzimidazole provide better anti-inflammatory pharmacology and improved toxicity profile

Benzimidazole is an important pharmacophore for clinically active drugs against inflammation and treatment of pain, however, it is associated with gastrointestinal side effects. Here we synthesized benzimidazole based agents with significant analgesic/anti-inflammatory potential but with less gastrointestinal adverse effects. In this study, we synthesized novel, orally bioavailable 2-mercaptobenzimidazole amino acid conjugates (4a-4o) and screened them for analgesic, anti-inflammatory and gastro-protective effects. The synthesized 2-mercaptbenzimidazole derivatives were characterized for their structure using FTIR, 1 H NMR and 13 C NMR spectroscopic techniques. The 2-mercaptobenzimidazole amino acid conjugates have found to possess potent analgesic, anti-inflammatory and gastroprotective activities, particularly with compound 4j and 4k. Most of the compounds exhibited remarkable anti-ulcer and antisecretory effects. Molecular docking studies were carried out to study the binding affinities and interactions of the synthesized compounds with target proteins COX-2 (PDB ID: 3LN1) and H+ /K+ -ATPase (PDB ID: 5Y0B). Our results support the clinical promise of these newly synthesized 2-mercaptobezimidazol conjugates as a component of therapeutic strategies for inflammation and analgesia, for which the gastric side effects are always a major limitation.

Synthesis, Biological Assessment, and Structure Activity Relationship Studies of New Flavanones Embodying Chromene Moieties

Novel flavanones that incorporate chromene motifs are synthesized via a one-step multicomponent reaction. The structures of the new chromenes are elucidated by using IR, ¹H-NMR, ¹³C-NMR, ¹H-¹H COSY, HSQC, HMBC, and elemental analysis. The new compounds are screened for their in vitro antimicrobial and cytotoxic activities. The antimicrobial properties are investigated and established against seven human pathogens, employing the agar well diffusion method and the minimum inhibitory concentrations. A majority of the assessed derivatives are found to exhibit significant antimicrobial activities against most bacterial strains, in comparison to standard reference drugs. Moreover, their cytotoxicity is appraised against four different human carcinoma cell lines: human colon carcinoma (HCT-116), human hepatocellular carcinoma (HepG-2), human breast adenocarcinoma (MCF-7), and adenocarcinoma human alveolar basal epithelial cell (A-549). All the desired compounds are subjected to in-silico studies, forecasting their drug likeness, bioactivity, and the absorption, distribution, metabolism, and excretion (ADME) properties prior to their synthetic assembly. The in-silico molecular docking evaluation of all the targeted derivatives is undertaken on gyrase B and the cyclin-dependent kinase. The in-silico predicted outcomes were endorsed by the in vitro studies.

Modeling Behavioral Experiment Interaction and Environmental Stimuli for a Synthetic C. elegans

This paper focusses on the simulation of the neural network of the Caenorhabditis elegans living organism, and more specifically in the modeling of the stimuli applied within behavioral experiments and the stimuli that is generated in the interaction of the C. elegans with the environment. To the best of our knowledge, all efforts regarding stimuli modeling for the C. elegansare focused on a single type of stimulus, which is usually tested with a limited subnetwork of the C. elegansneural system. In this paper, we follow a different approach where we model a wide-range of different stimuli, with more flexible neural network configurations and simulations in mind. Moreover, we focus on the stimuli sensation by different types of sensory organs or various sensory principles of the neurons. As part of this work, most common stimuli involved in behavioral assays have been modeled. It includes models for mechanical, thermal, chemical, electrical and light stimuli, and for proprioception-related self-sensed information exchange with the neural network. The developed models have been implemented and tested with the hardware-based Si elegans simulation platform.