Discovery of Potential Inhibitors of CDK1 by Integrating Pharmacophore-Based Virtual Screening, Molecular Docking, Molecular Dynamics Simulation Studies, and Evaluation of Their Inhibitory Activity.

The ability of CDK1 to compensate for the absence of other cell cycle CDKs poses a great challenge to treat cancers that overexpress these proteins. Despite several studies focusing on the area, there are no FDA-approved drugs selectively targeting CDK1. Here, the study aimed to develop potential CDK1 selective inhibitors through drug repurposing and leveraging the structural insights provided by the hit molecules generated. Approximately 280,000 compounds from DrugBank, Selleckchem, Otava and an in-house library were screened initially based on fit values using 3D QSAR pharmacophores built for CDK1 and subsequently through Lipinski, ADMET, and TOPKAT filters. 10,310 hits were investigated for docking into the binding site of CDK1 determined using the crystal structure of human CDK1 in complex with NU6102. The best 55 hits with better docking scores were further analyzed, and 12 hits were selected for 100 ns MD simulations followed by binding energy calculations using the MM-PBSA method. Finally, 10 hit molecules were tested in an in vitro CDK1 Kinase inhibition assay. Out of these, 3 hits showed significant CDK1 inhibitory potential with IC50 < 5 µM. These results indicate these compounds can be used to develop subtype-selective CDK1 inhibitors with better efficacy and reduced toxicities in the future.

Uncovering the role of aquaporin and chromobox family members as potential biomarkers in head and neck squamous cell carcinoma via integrative multiomics and in silico approach.

Head and neck squamous cell carcinoma (HNSC) is a diverse group of tumors arising from oral cavity, oropharynx, larynx, and hypopharynx squamous epithelium, posing significant morbidity. Aquaporins (AQPs) are membrane proteins forming water channels, some associated with carcinomas. Chromobox (CBX) family is known to modulate physiological and oncological processes. In our study, we analyzed AQPs and CBXs having significant expression followed by their prognostic and mutational assessment. Next, we performed enrichment and tumor infiltration analysis followed by HPA validation. Lastly, we established a 3-node miRNA-TF-mRNA regulatory network and performed protein-protein docking of the highest-degree subnetwork motif between TF and mRNA. Significant upregulation of CBX3/2 and downregulation of AQP3/5/7 correlated with poor overall survival (OS) in HNSC patients. The most significant pathway, GO-BP, GO-MF, and GO-CC terms associated with AQP3 and CBX3 were passive transport by aquaporins, response to vitamin, glycerol channel activity, and condensed chromosome, centromeric region. AQP3 negatively correlated with [Formula: see text] T cells, positively with [Formula: see text] T cells and B cells, and negatively with tumor purity, whereas CBX3 positively correlated with [Formula: see text] T cells, negatively with [Formula: see text] T cells and B cells, and positively with tumor purity. Three-node miRNA-TF-mRNA regulatory network revealed a highest-degree subnetwork motif comprising one TF (SMAD3), one miRNA (miR-423-5p), and one mRNA (AQP3). Protein-protein interaction studies suggested a direct interaction between AQP3 and Smad3 proteins. We concluded that AQP3 and CBX3 hold potential as treatment strategies and individual prognostic biomarkers, while further protein-protein interaction studies of AQP3 could offer insights into its interactions with Smad3 proteins.

Computational studies to explore inhibitors against the cyclin-dependent kinase 12/13 enzyme: an insilco pharmacophore modeling, molecular docking and dynamics approach.

Cancer is enlisted among the deadliest disease all over the world. The cyclin-dependent kinases 12 and 13 have been identified as cell cycle regulators. They conduct transcription and co-transcriptional processes by phosphorylating the C-terminal of RNA polymerase-II. Inhibition of CDK12 and 13 selectively presents a novel strategy to treat triple-negative breast cancer, but dual inhibitors are still lacking. Here, we report the screening of the natural product compound class against the dual CDK12/13 enzyme by employing various in silico methods. Complexes of CDK12 enzymes are used to form common feature pharmacophore models, whereas we perform receptor-based pharmacophore modelling on CDK13 enzyme owing to the availability of a single PDB. On conducting screening over the representative pharmacophores, the common drug-like screened natural products were shortlisted for conducting molecular docking studies. After molecular docking calculations, the candidates that showed crucial interaction with CDK12 and CDK13 enzymes were shortlisted for simulation studies. Five common docked candidates were selected for molecular dynamics simulations and free energy calculations. Based on the cut-off criteria of free energy calculations, one common hit was selected as the dual CDK12/13 inhibitor. The outcome concluded that the hit with ID CNP0386383 possesses drug-like properties, displays crucial interaction in the binding pocket, and shows stable dynamic behaviour and higher binding energy than the experimentally reported inhibitor of both CDK12 and CDK13 enzymes.Communicated by Ramaswamy H. Sarma.

Targeting allosteric binding site in methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) to identify natural product inhibitors via structure-based computational approach.

Cancer has been viewed as one of the deadliest diseases worldwide. Among various types of cancer, breast cancer is the most common type of cancer in women. Methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) is a promising druggable target and is overexpressed in cancerous cells, like, breast cancer. We conducted structure-based modeling on the allosteric site of the enzyme. Targeting the allosteric site avoids the problem of drug resistance. Pharmacophore modeling, molecular docking, HYDE assessment, drug-likeness, ADMET predictions, simulations, and free-energy calculations were performed. The RMSD, RMSF, RoG, SASA, and Hydrogen-bonding studies showed that seven candidates displayed stable behaviour. As per the literature, average superimposed simulated structures revealed a similar protein conformational change in the αE'-ßf' loop, causing its displacement away from the allosteric site. The MM-PBSA showed tight binding of six compounds with the allosteric pocket. The effect of inhibitors interacting in the allosteric site causes a decrease in the binding energy of J49 (active-site inhibitor), suggesting the effect of allosteric binding. The PCA and FEL analysis revealed the significance of the docked compounds in the stable behaviour of the complexes. The outcome can contribute to the development of potential natural products with drug-like properties that can inhibit the MTHFD2 enzyme.

Balancing water and radiation productivity suggests a clue for improving yields in wheat under combined water deficit and terminal heat stress.

Sustaining crop yield under abiotic stresses with optimized resource use is a prerequisite for sustainable agriculture, especially in arid and semi-arid areas. Water and heat stress are major abiotic stresses impacting crop growth and yield by influencing complex physiological and biochemical processes during the life cycle of crops. In a 2-year (2015-2017) research, spring wheat cv. HD-2967 was grown under deficit irrigation and delayed sowing conditions to impose water and terminal heat stresses, respectively. The data were analyzed for seasonal crop water use, radiation interception, water productivity (WP), and radiation productivity (RP) under combined water deficit and terminal heat stresses. Seasonal crop water use was significantly affected by stresses in the order of water + terminal heat > water > terminal heat. Water stress showed minimal effect on the light extinction coefficient and consequently on seasonal intercepted photosynthetically active radiation (IPAR). However, seasonal IPAR was primarily affected by combined water + terminal heat and terminal heat stress alone. The slope of crop water use and IPAR, i.e., canopy conductance, an indicator of canopy stomatal conductance, was more influenced by water stress than by terminal heat stress. Results showed that linear proportionality between WP and RP is no longer valid under stress conditions, as it follows a curvilinear relation. This is further supported by the fact that independent productivity (either water or radiation) lacked the ability to explain variability in the final economic yield or biomass of wheat. However, the ratio of RP to WP explained the variability in wheat yield/biomass under individual or combined stresses. This suggests a clue for improving higher wheat yield under stress by managing WP and RP. The highest biomass or yield is realized when the ratio of RP to WP approaches unity. Screening of genotypes for traits leading to a higher ratio of RP to WP provides an opportunity for improving wheat productivity under stressed environments.

Identifying natural product inhibitors against CDK9 enzyme via combined multicomplex-based pharmacophore modeling, interaction studies and molecular dynamics simulations.

In the current work, multicomplex-based pharmacophore modeling was performed on the CDK9 enzyme. The generated models possess five, four, and six features, which were subjected to the validation process. Among them, six feature models were selected as representative models to conduct the virtual screening process. The screened drug-like candidates were chosen to perform molecular docking to study their interaction patterns within the binding cavity of the CDK9 protein. Based on the docking score and presence of crucial interactions, out of 780 filtered candidates, only 205 were docked. These docked candidates were further accessed via HYDE assessment. Based on ligand efficiency and Hyde score, only nine candidates passed the criteria. The stability of these nine complexes, along with the reference, was studied by molecular dynamics simulations. Out of nine, only seven displayed stable behaviour during the simulations, and their stability was further assessed by molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA)-based free binding energy calculations and per residue contribution. From the present contribution, we obtained seven unique scaffolds that can be utilized as the starting lead for the development of CDK9 anticancer compounds.

Targeting Apoptotic Pathway of Cancer Cells with Phytochemicals and Plant-Based Nanomaterials.

Apoptosis is the elimination of functionally non-essential, neoplastic, and infected cells via the mitochondrial pathway or death receptor pathway. The process of apoptosis is highly regulated through membrane channels and apoptogenic proteins. Apoptosis maintains cellular balance within the human body through cell cycle progression. Loss of apoptosis control prolongs cancer cell survival and allows the accumulation of mutations that can promote angiogenesis, promote cell proliferation, disrupt differentiation, and increase invasiveness during tumor progression. The apoptotic pathway has been extensively studied as a potential drug target in cancer treatment. However, the off-target activities of drugs and negative implications have been a matter of concern over the years. Phytochemicals (PCs) have been studied for their efficacy in various cancer cell lines individually and synergistically. The development of nanoparticles (NPs) through green synthesis has added a new dimension to the advancement of plant-based nanomaterials for effective cancer treatment. This review provides a detailed insight into the fundamental molecular pathways of programmed cell death and highlights the role of PCs along with the existing drugs and plant-based NPs in treating cancer by targeting its programmed cell death (PCD) network.

US Food and Drug Administration Approval Summary: Fam-Trastuzumab Deruxtecan-nxki for Human Epidermal Growth Factor Receptor 2-Low Unresectable or Metastatic Breast Cancer.

PURPOSE: The US Food and Drug Administration approved fam-trastuzumab deruxtecan-nxki (DS-8201a, T-DXd) for the treatment of adult patients with unresectable or metastatic human epidermal growth factor receptor 2 (HER2)-low (immunohistochemistry 1 + or immunohistochemistry 2+/in situ hybridization-) breast cancer who have received a prior chemotherapy in the metastatic setting or developed disease recurrence during or within 6 months of completing adjuvant chemotherapy. PATIENTS AND METHODS: Approval was based on DESTINY-Breast04, a phase III, randomized, open-label, multicenter trial in patients with unresectable or metastatic HER2-low breast cancer, determined at a central laboratory. A total of 557 patients were randomly assigned (2:1) to receive either T-DXd 5.4 mg/kg intravenously once every 3 weeks (n = 373) or physicians' choice of chemotherapy (n = 184). RESULTS: The study met its primary efficacy end point of progression-free survival (PFS) by blinded independent central review assessment in the hormone receptor-positive (HR+) cohort (N = 494) with an estimated hazard ratio (HR) of 0.51(95% CI, 0.40 to 0.64; P < .0001). Key secondary end points were also met, including PFS in the intent-to-treat population with an HR of 0.50 (95% CI, 0.40 to 0.63; P < .0001), overall survival (OS) in the HR+ cohort with an HR of 0.64 (95% CI, 0.48 to 0.86; P = .0028) and OS in the intent-to-treat with an HR of 0.64 (95% CI, 0.49 to 0.84; P = .0010). The safety profile of T-DXd was consistent with previously approved indications, and no new safety signals were observed in this study population. CONCLUSION: The approval of T-DXd in HER2-low metastatic breast cancer was based on statistically significant and clinically meaningful PFS and OS improvements observed in the DESTINY-Breast04 trial and represents the first approved therapy specifically for the treatment of HER2-low metastatic breast cancer.

Systems biology of chromium-plant interaction: insights from omics approaches.

Plants are frequently subjected to heavy metal (HM) stress that impedes their growth and productivity. One of the most common harmful trace metals and HM discovered is chromium (Cr). Its contamination continues to increase in the environment due to industrial or anthropogenic activities. Chromium is severely toxic to plant growth and development and acts as a human carcinogen that enters the body by inhaling or taking Cr-contaminated food items. Plants uptake Cr via various transporters, such as sulfate and phosphate transporters. In nature, Cr is found in various valence states, commonly Cr (III) and Cr (VI). Cr (VI) is soil's most hazardous and pervasive form. Cr elevates reactive oxygen species (ROS) activity, impeding various physiological and metabolic pathways. Plants have evolved various complex defense mechanisms to prevent or tolerate the toxic effects of Cr. These defense mechanisms include absorbing and accumulating Cr in cell organelles such as vacuoles, immobilizing them by forming complexes with organic chelates, and extracting them by using a variety of transporters and ion channels regulated by various signaling cascades and transcription factors. Several defense-related proteins including, metallothioneins, phytochelatins, and glutathione-S-transferases aid in the sequestration of Cr. Moreover, several genes and transcriptional factors, such as WRKY and AP2/ERF TF genes, play a crucial role in defense against Cr stress. To counter HM-mediated stress stimuli, OMICS approaches, including genomics, proteomics, transcriptomics, and metallomics, have facilitated our understanding to improve Cr stress tolerance in plants. This review discusses the Cr uptake, translocation, and accumulation in plants. Furthermore, it provides a model to unravel the complexities of the Cr-plant interaction utilizing system biology and integrated OMICS approach.

Structural differences in 3C-like protease (Mpro) from SARS-CoV and SARS-CoV-2: molecular insights revealed by Molecular Dynamics Simulations.

Novel coronavirus SARS-CoV-2 has infected millions of people with thousands of mortalities globally. The main protease (Mpro) is vital in processing replicase polyproteins. Both the CoV's Mpro shares 97% identity, with 12 mutations, but none are present in the active site. Although many therapeutics and vaccines are available to combat SARS-CoV-2, these treatments may not be practical due to their high mutational rate. On the other hand, Mpro has a high degree of conservation throughout variants, making Mpro a stout drug target. Here, we report a detailed comparison of both the monomeric Mpro and the biologically active dimeric Mpro using MD simulation to understand the impact of the 12 divergent residues (T35V, A46S, S65N, L86V, R88K, S94A, H134F, K180N, L202V, A267S, T285A and I286L) on the molecular microenvironment and the interaction between crucial residues. The present study concluded that the change in the microenvironment of residues at the entrance (T25, T26, M49 and Q189), near the catalytic site (F140, H163, H164, M165 and H172) and in the substrate-binding site (V35, N65, K88 and N180) is due to 12 mutations in the SARS-CoV-2 Mpro. Furthermore, the involvement of F140, E166 and H172 residues in dimerization stabilizes the Mpro dimer, which should be considered. We anticipate that networks and microenvironment changes identified here might guide repurposing attempts and optimization of new Mpro inhibitors. Supplementary Information: The online version contains supplementary material available at 10.1007/s11224-022-02089-6.

Reckoning apigenin and kaempferol as a potential multi-targeted inhibitor of EGFR/HER2-MEK pathway of metastatic colorectal cancer identified using rigorous computational workflow.

In the past two decades, the treatment of metastatic colorectal cancer (mCRC) has been revolutionized as multiple cytotoxic, biological, and targeted drugs are being approved. Unfortunately, tumors treated with single targeted agents or therapeutics usually develop resistance. According to pathway-oriented screens, mCRC cells evade EGFR inhibition by HER2 amplification and/or activating Kras-MEK downstream signaling. Therefore, treating mCRC patients with dual EGFR/HER2 inhibitors, MEK inhibitors, or the combination of the two drugs envisaged to prevent the resistance development which eventually improves the overall survival rate. In the present study, we aimed to screen potential phytochemical lead compounds that could multi-target EGFR, HER2, and MEK1 (Mitogen-activated protein kinase kinase) using a computer-aided drug design approach that includes molecular docking, endpoint binding free energy calculation using MM-GBSA, ADMET, and molecular dynamics (MD) simulations. Docking studies revealed that, unlike all other ligands, apigenin and kaempferol exhibit the highest docking score against all three targets. Details of ADMET analysis, MM/GBSA, and MD simulations helped us to conclusively determine apigenin and kaempferol as potentially an inhibitor of EGFR, HER2, and MEK1 apigenin and kaempferol against mCRC at a systemic level. Additionally, both apigenin and kaempferol elicited antiangiogenic properties in a dose-dependent manner. Collectively, these findings provide the rationale for drug development aimed at preventing CRC rather than intercepting resistance.

Integrative multiomics and in silico analysis revealed the role of ARHGEF1 and its screened antagonist in mild and severe COVID-19 patients.

COVID-19 is a sneaking deadly disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The rapid increase in the number of infected patients worldwide enhances the exigency for medicines. However, precise therapeutic drugs are not available for COVID-19; thus, exhaustive research is critically required to unscramble the pathogenic tools and probable therapeutic targets for the development of effective therapy. This study utilizes a chemogenomics strategy, including computational tools for the identification of viral-associated differentially expressed genes (DEGs), and molecular docking of potential chemical compounds available in antiviral, anticancer, and natural product-based libraries against these DEGs. We scrutinized the messenger RNA expression profile of SARS-CoV-2 patients, publicly available on the National Center for Biotechnology Information-Gene Expression Omnibus database, stratified them into different groups based on the severity of infection, superseded by identification of overlapping mild and severe infectious (MSI)-DEGs. The profoundly expressed MSI-DEGs were then subjected to trait-linked weighted co-expression network construction and hub module detection. The hub module MSI-DEGs were then exposed to enrichment (gene ontology + pathway) and protein-protein interaction network analyses where Rho guanine nucleotide exchange factor 1 (ARHGEF1) gene conjectured in all groups and could be a probable target of therapy. Finally, we used the molecular docking and molecular dynamics method to identify inherent hits against the ARHGEF1 gene from antiviral, anticancer, and natural product-based libraries. Although the study has an identified significant association of the ARHGEF1 gene in COVID19; and probable compounds targeting it, using in silico methods, these targets need to be validated by both in vitro and in vivo methods to effectively determine their therapeutic efficacy against the devastating virus.

Oral Health Status and Treatment Need in Geriatric Patients with Different Degrees of Cognitive Impairment and Dementia: A Cross-Sectional Study.

BACKGROUND: Health can be defined as more than an absence or lack of disease. It is generally related to personal, physical, social, along with spiritual wellness. However, the importance of good health is comparable with a progressive physical and cognitive limitations due to aging and hence, its clear definition is not possible. Hence, most of the important aims or goals in aging are unrelated to finding a cure but rather toward achieving an optimal function. Thus, a healthy aging process that encompasses physical, mental, psychological, and spiritual well-being is always much desired. AIM AND OBJECTIVES: The aim and objective of this study is to assess the oral health status and degree of cognitive impairment along with dementia, if present. MATERIALS AND METHODS: This is a prospective and cross-sectional analysis comprising of 300 study participants of which 150 are males while 150 are females. Cognitive ability is assessed using the Standardized Mini-Mental State Examination (SMMSE) scoring test. A score value lesser than or equal to 23 is considered as low, whereas a score of 24 and above represents normal cognitive abilities. Subjects with low score are selected for the study. Oral health status is assessed by examining a) total numbers of teeth present; b) presence or absence of denture use; and c) capacity for masticatory or chewing ability (recorded as yes or no). Demographic variables parameters include age, gender, and presence of smoking habit. Clinical parameters or variables are analyzed by employing the independent t-test and Chi-square test. Pearson's correlation analysis is used to test a correlation between impairment of cognitive capacity, oral health status, masticatory capability, and use of dentures, if present. Two-tailed t-test is used to derive a P value for significance. RESULTS: The total numbers of teeth present are significantly correlated with a lower SMMSE score (R = + 0.56; P = 0.03) while a significant association is noted between ability for mastication and lower SMMSE score (P = 0.05). CONCLUSION: This study concluded that loss of cognition or dementia is closely related to a poor oral health status.

New simple molecular fluorescent probes for rapid and highly selective sensing of hydrazine by aggregate-induced emission.

With an aim towards the design of efficient and straightforward fluorescent probes for hydrazine, the synthesis of (2-acetoxyaryl) methylene diacetate derivatives (1-4) was carried out by reacting substituted aromatic α-hydroxy aldehydes with acetyl chloride and sodium acetate in excellent yields. As a preliminary investigation, the ability of probe 1 was examined for the detection of substituted aliphatic and aromatic amines, amino acids, and other ions in Britton-Robinson buffer solution (50 mM, water/ethanol v/v of 99/1 at pH 7.4). Probe 1 selectively exhibited an intense blue fluorescence with hydrazine in less than 2 minutes, whereas light green or no fluorescence was noticed with substituted amines and amino acids. Among all the probes employed (1-4) in the present study, probes 1 and 2 were found efficient towards the rapid detection of hydrazine. Furthermore, the fluorescence sensing ability of probes 1 and 2 was tested not only under varying pH conditions but also by varying water-fraction from 0-99%. Moreover, the detection limits of hydrazine using 1 and 2 were found as 8.4 and 8.7 ppb, respectively, which is less than the acceptable limit as per the standards of the US Environment Protection Agency. In this contribution, the probes 1 and 2 demonstrate rapid, selective, sensitive, and ratiometric detection of highly toxic hydrazine by OFF-ON fluorescence switch in water samples as well as living cells.

Structure-based identification of novel sirtuin inhibitors against triple negative breast cancer: An in silico and in vitro study.

Triple-negative breast cancer (TNBC) is an aggressive disease exemplified by a poor prognosis, greater degrees of relapse, the absence of hormonal receptors for coherent utilization of targeted therapy, poor response to currently available therapeutics and development of chemoresistance. Aberrant activity of sirtuins (SIRTs) has strong implications in the metastatic and oncogenic progression of TNBC. Synthetic SIRT inhibitors are effective, however, they have shown adverse side effects emphasizing the need for plant-derived inhibitors (PDIs). In the current study, we identified potential plant-derived sirtuin inhibitors using in silico approach i.e. molecular docking, ADMET and molecular dynamics simulations (MD). Docking studies revealed that Sulforaphane, Kaempferol and Apigenin exhibits the highest docking scores against SIRT1 & 5, 3 and 6 respectively. ADMET analysis of above hits demonstrated drug-like profile. MD of prioritized SIRTs-PDIs complexes displayed stability with insignificant deviations throughout the trajectory. Furthermore, we determined the effect of our prioritized molecules on cellular viability, global activity as well as protein expression of sirtuins and stemness of TNBC cells utilizing in vitro techniques. Our in vitro findings complements our in silico results. Collectively, these findings provide a better insight into the structural basis of sirtuin inhibition and can facilitate drug design process for TNBC management.

Combined comparative molecular field analysis, comparative molecular similarity indices analysis, molecular docking and molecular dynamics studies of histone deacetylase 6 inhibitors.

Human histone deacetylase isoform 6 (HDAC6) has been shown to have an immense role in cell motility and aggresome formation and is being an attractive selective target for the treatment of multiple tumour types and neurodegenerative conditions. The discovery of selective HDAC6 inhibitors with new chemical functionalities is therefore of utmost interest to researchers. In order to examine the structural requirements for HDAC6-specific inhibitors and to derive predictive model which can be used for designing new selective HDAC6 inhibitors, a three-dimensional quantitative structure-activity relationship study was carried out on a diverse set of ligands using common feature-based pharmacophore alignment followed by employing comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) techniques. The models displayed high correlation of 0.978 and 0.991 for best CoMFA and CoMSIA models, respectively, and a good statistical significance. The model could be used for predicting activities of the test set compounds as well as for deriving useful information regarding steric, electrostatic, hydrophobic properties of the molecules used in this study. Further, the training and test set molecules were docked into the HDAC6 binding site and molecular dynamics was carried out to suggest structural requirements for design of new inhibitors.

A DFT study of inclusion complexes of substituted calix[n]arenes with dasatinib and lapatinib.

Herein, we have presented the results of Density Functional Theory (DFT) based calculations of inclusion complexes of lapatinib and dasatinib with calix[n]arene macrocycles. A total of 48 calix [n]arene complexes were modeled via considering varied ring sizes (n = 4,5,6,8) and upper-rim functionalization viz. SO3H, tert-Butyl, iso-Propyl, COOH, C2H5OH, and C2H5NH2. From the results of multilevel molecular docking, DFT energetics, and reactivity descriptors; it has been demonstrated that dasatinib form optimal complexes with calix 4f, 3f (-35 to -40 kcal/mol). Moreover, for lapatinib, hosts 3f, 4a, 1f, 3d have the capability to generate promising complexes (>35 kcal/mol). Based on counterpoise corrected binding energies (Ebind) and global reactivity descriptors, we anticipate that the proposed complexes can vitally be used as analogous to carrier-mediated-drug-delivery.

Molecular dynamics-assisted pharmacophore modeling of caspase-3-isatin sulfonamide complex: Recognizing essential intermolecular contacts and features of sulfonamide inhibitor class for caspase-3 binding.

The identification of isatin sulfonamide as a potent small molecule inhibitor of caspase-3 had fuelled the synthesis and characterization of the numerous sulfonamide class of inhibitors to optimize for potency. Recent works that relied on the ligand-based approaches have successfully shown the regions of optimizations for sulfonamide scaffold. We present here molecular dynamics-based pharmacophore modeling of caspase-3-isatin sulfonamide crystal structure, to elucidate the essential non-covalent contacts and its associated pharmacophore features necessary to ensure caspase-3 optimal binding. We performed 20ns long dynamics of this crystal structure to extract global conformation states and converted into structure-based pharmacophore hypotheses which were rigorously validated using an exclusive focussed library of experimental actives and inactives of sulfonamide class by Receiver Operating Characteristic (ROC) statistic. Eighteen structure-based pharmacophore hypotheses with better sensitivity and specificity measures (>0.6) were chosen which collectively showed the role of pocket residues viz. Cys163 (S1 sub-site; required for covalent and H bonding with Michael acceptor of inhibitors), His121 (S1; π stack with bicyclic isatin moiety), Gly122 (S1; H bond with carbonyl oxygen) and Tyr204 (S2; π stack with phenyl group of the isatin sulfonamide molecule) as stringent binding entities for enabling caspase-3 optimal binding. The introduction of spatial pharmacophore site points obtained from dynamics-based pharmacophore models in a virtual screening strategy will be helpful to screen and optimize molecules belonging to sulfonamide class of caspase-3 inhibitors.

Identification of potent cholecystokinin-B receptor antagonists: synthesis, molecular modeling and anti-cancer activity against pancreatic cancer cells.

Advanced malignant stages of pancreatic cancer have poor prognosis and very few treatment strategies are available. Pancreatic cancer is known to possess unique growth-related receptors that when activated, stimulate tumour proliferation. Gastrin and its related peptide cholecystokinin (CCK) are also significantly involved in the growth of this cancer type as well as other malignancies through activation of the cholecystokinin-B receptor (CCK-BR). New treatment strategies with CCK-BR antagonists are being suggested that suppress the growth promoting effects of gastrin. In this paper, we report the development of two series of quinazolinone derivatives incorporating hydrazinecarbothioamide (compounds 3a-g) and the hydrazino group (compounds 4a-e) as linkers for developing CCK-BR antagonists. The affinities of the compounds were determined using docking into the CCK-BR homology modeled structure. The compounds were tested for in vitro CCK-BR binding and gastric acid secretion in an isolated lumen-perfused mouse stomach assay. The compounds exhibited CCK-BR binding activity (IC50) in the range of 0.2-975 nM and showed good gastric acid secretion inhibitory activity. Molecular modeling of the compounds was done and pharmacophore mapping results showed good prediction of in vitro activity which correlated well with the experimental antagonistic activity. The compounds were further tested for their cytotoxicity on CCK-BR expressing pancreatic cancer cells. The results of the study provided two potent CCK-BR antagonists which also possess good to moderate growth inhibitory activities against pancreatic cancer cells.

Molecular mechanisms and mode of tamoxifen resistance in breast cancer.

Breast cancer is one of the most common cancers in women around the globe Tamoxifen is used for the last 40 years as an endocrine therapy for breast cancer. This resulted in the reduction of mortality rate by 30% and it still remains one of the most effective therapies against breast cancer. However, resistance against tamoxifen is still one of the major hurdles in the effective management of breast cancer. Intense research has been conducted in the past decade to further explore its resistance mechanism, but still a lot of research will be needed to effectively alleviate this problem. Several biochemical factors and molecular pathways, such as the modulation of ER signaling, upregulation of growth factors had been observed as key factors for tamoxifen resistance (TR). After, initial therapy of five to ten years, breast cancer patients develops resistance towards this drug. The resistance leads to the development of other cancers like uterine cancer. Here, we briefly explore all the molecular events related to tamoxifen resistance and focus on its mechanism of action as well as other pharmacological approaches to better its beneficial effects in the treatment of breast carcinoma.