Biochemistry And Microbial Sciences - Research Publications
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Item Bioinformatics insights into CENP-T and CENP-W protein-protein interaction disruptive amino acid substitution in the CENP-T-W complex(John Wiley and Sons Inc, 2023-11-09T00:00:00) Mohanty, Suryakanta; Bhadane, Rajendra; Kumar, ShashankKinetochores are multi-protein assemblies present at the centromere of the human chromosome and play a crucial role in cellular mitosis. The CENP-T and CENP-W chains form a heterodimer, which is an integral part of the inner kinetochore, interacting with the linker DNA on one side and the outer kinetochore on the other. Additionally, the CENP-T-W dimer interacts with other regulatory proteins involved in forming inner kinetochores. The specific roles of different amino acids in the CENP-W at the protein-protein interaction (PPI) interface during the CENP-T-W dimer formation remain incompletely understood. Since cell division goes awry in diseases like cancer, this CENP-T-W partnership is a potential target for new drugs that could restore healthy cell division. We employed molecular docking, binding free energy calculations, and molecular dynamics (MD) simulations to investigate the disruptive effects of amino acids substitutions in the CENP-W chain on CENP-T-W dimer formation. By conducting a molecular docking study and analysing hydrogen bonding interactions, we identified key residues in CENP-W (ASN-46, ARG-53, LEU-83, SER-86, ARG-87, and GLY-88) for further investigation. Through site-directed mutagenesis and subsequent binding free energy calculations, we refined the selection of mutant. We chose four mutants (N46K, R53K, L83K, and R87E) of CENP-W to assess their comparative potential in forming CENP-T-W dimer. Our analysis from 250 ns long revealed that the substitution of LEU83 and ARG53 residues in CENP-W with the LYS significantly disrupts the formation of CENP-T-W dimer. In conclusion, LEU83 and ARG53 play a critical role in CENP-T and CENP-W dimerization which is ultimately required for cellular mitosis. Our findings not only deepen our understanding of cell division but also hint at exciting drug-target possibilities. � 2023 The Authors. Journal of Cellular Biochemistry published by Wiley Periodicals LLC.Item Immunodominant conserved moieties on spike protein of SARS-CoV-2 renders virulence factor for the design of epitope-based peptide vaccines(Springer, 2023-11-23T00:00:00) Mohapatra, Subhashree; Kumar, Santosh; Kumar, Shashank; Singh, Atul Kumar; Nayak, BismitaThe outbreak of novel SARS-CoV-2 virion has wreaked havoc with a high prevalence of respiratory illness and high transmission due to a vague understanding of the viral antigenicity, augmenting the dire challenge to public health globally. This viral member necessitates the expansion of diagnostic and therapeutic tools to track its transmission and confront it through vaccine development. Therefore, prophylactic strategies are mandatory. Virulent spike proteins can be the most desirable candidate for the computational design of vaccines targeting SARS-CoV-2, followed by the meteoric development of immune epitopes. Spike protein was characterized using existing bioinformatics tools with a unique roadmap related to the immunological profile of SARS-CoV-2 to predict immunogenic virulence epitopes based on antigenicity, allergenicity, toxicity, immunogenicity, and population coverage. Applying in silico approaches, a set of twenty-four B lymphocyte-based epitopes and forty-six T lymphocyte-based epitopes were selected. The predicted epitopes were evaluated for their intrinsic properties. The physico-chemical characterization of epitopes qualifies them for further in vitro and in vivo analysis and pre-requisite vaccine development. This study presents a set of screened epitopes that bind to HLA-specific allelic proteins and can be employed for designing a peptide vaccine construct against SARS-CoV-2 that will confer vaccine-induced protective immunity due to its structural stability. � 2023, The Author(s), under exclusive licence to Indian Virological Society.Item Synthesis, In silico mapping for anti-cancer proviso, hardness studies of D-gluconic acid monohydrate crystals for usage in electronic, mechanical and biological sectors(Elsevier Ltd, 2023-10-17T00:00:00) B, Padmanaban; Nikolova, Maria P.; Kumar, Shashank; K, SenthilKannanD-Gluconic acid monohydrate - DGAMH crystals are grown in a period of 61 days by using the customary slow evaporation method with a, b and c as 8.4309, 5.409 and 10.4071 in � units; ? as 96.87�; monoclinic system, space group as P21. The material is an anticancer stipulation to inhibit them with the docked score of the DGAMH as ?6.0 and ?7.1 for both cases. Considering the mechanic behaviour of the DGAMH; the n as 7.57 of the DGAMH � work hardening coefficient value as Reverse ISE (indentation size effect) response for DGAMH. The computational structural info of DGAMH provides the supercell proviso, VanderWaal's impact with the nano-tubular proviso of DGAMH for cell impacting, weak type of interactions and devices with nano-tube impact. The electronic fluxing is in microns for macro-DGAMH; micro-DGAMH; thin-film DGAMH and nano-DGAMH for filtering property confirmations. The frequency by IC741 is twice over the input values with DGAMH crystal. � 2023 The AuthorsItem Piper chaba, an Indian spice plant extract, inhibits cell cycle G1/S phase transition and induces intrinsic apoptotic pathway in luminal breast cancer cells(John Wiley and Sons Ltd, 2023-09-15T00:00:00) Prajapati, Kumari Sunita; Kumar, ShashankPiper chaba (Piperaceae) is a medicinal spice plant that possesses several pharmacological activities. In the present study, we for the first time studied the effect of P. chaba extract on breast cancer cells. P. chaba stem methanolic (PCSM) extract produced time and dose dependent cytotoxicity in luminal breast cancer cells (MCF-7 and T47D) with a minimal toxicity in breast normal cells (MCF-10A) at 10�100 �g/mL concentration. PCSM extract exerts 16.79 and 31.21 �g/mL IC50 for T47D and MCF-7 cells, respectively, in 48 h treatment. PCSM significantly arrests the T47D cells at the G0/G1 phase by reducing the CCND1 and CDK4 expression at mRNA and protein levels. PCSM extract treatment significantly altered nuclear morphology, mitochondria membrane potential, and production of reactive oxygen species in T47D cells at IC50 concentration. Extract treatment significantly altered the Bax/Bcl-2 ratio and altered caspase 8 and 3 mRNA/protein levels in T47D cells. Confocal microscopy showed an increase in late apoptosis in PCSM extract-treated breast cancer cells at IC50. Further, an increased caspase 9 and caspase 3/7 enzymatic activity was observed in test cells compared with nontreated cells. In conclusion, P. chaba phytocompound possesses the potential to induce cell cycle arrest and induce apoptosis in luminal breast cancer cells. � 2023 John Wiley & Sons Ltd.Item Designing of neoepitopes based vaccine against breast cancer using integrated immuno and bioinformatics approach(Taylor and Francis Ltd., 2023-08-16T00:00:00) Shuaib, Mohd; Singh, Atul Kumar; Gupta, Sanjay; Alasmari, Abdullah F.; Alqahtani, Flaeh; Kumar, ShashankCancer is characterized by genetic instability due to accumulation of somatic mutations in the genes which generate neoepitopes (mutated epitopes) for targeting by Cytotoxic T lymphocytes (CTL). Breast cancer has a high transformation rate with unique composition of mutational burden and neoepitopes load that open a platform to designing a neoepitopes-based vaccine. Neoepitopes-based therapeutic cancer vaccines designed by neoantigens have shown to be feasible, nontoxic, and immunogenic in cancer patients. Stimulation of CTL by neoepitope-based vaccine of self-antigenic proteins plays a key role in distinguishing cancer cells from normal cells and selectively targets only malignant cells. A neoepitopes-based vaccine to combat breast cancer was designed by combining immunology and bioinformatics approaches. The vaccine construct was assembled by the fusion of CTL neoepitopes, helper sequences (used for better separation of the epitopes), and adjuvant together with linkers. The neoepitopes were identified from somatic mutations in the MUC16, TP53, RYR2, F5, DNAH17, ASPM, and ABCA13 self-antigenic proteins. The vaccine construct was undertaken to study the immune simulations (IS), physiochemical characteristics (PP), molecular docking (MD) and simulations, and cloning in appropriate vector. Together, these parameters establish safety, stability, and a strong binding affinity against class I MHC molecules capable of inducing a complete immune response against breast cancer cells. Communicated by Ramaswamy H. Sarma. � 2023 Informa UK Limited, trading as Taylor & Francis Group.Item Loss of miR-6844 alters stemness/self-renewal and cancer hallmark(s) markers through CD44-JAK2-STAT3 signaling axis in breast cancer stem-like cells(John Wiley and Sons Inc, 2023-07-12T00:00:00) Prajapati, Kumari Sunita; Kumar, ShashankMicroRNAs regulate breast stemness and self-renewal properties in breast cancer cells at the molecular level. Recently we reported the clinical relevance and in vitro expression profile of novel miR-6844 in breast cancer and -derived stem-like cells (mammosphere). In the present study, we first time explore the functional role of loss of miR-6844 in breast cancer cells derived mammosphere. Down expression of miR-6844 significantly decreased cell proliferation in MCF-7 and T47D cells derived mammosphere in a time-dependent manner. MiR-6844 down expression reduced the sphere formation in terms of size and number in test cells. Loss of miR-6844 significantly altered stemness and self-renewal markers (Bmi-1, Nanog, c-Myc, Sox2, and CD44) in mammosphere compared to negative control spheres. Moreover, loss of miR-6844 inhibits the JAK2-STAT3 signaling pathway by decreasing p-JAK2 and p-STAT3 levels in breast cancer cells derived mammosphere. Loss of miR-6844 expression significantly decreased CCND1 and CDK4 mRNA/protein levels and arrested breast cancer stem-like cells in G2/M phase. Reduced expression of miR-6844 increased Bax/Bcl-2 ratio, late apoptotic cell population, and Caspase 9 and 3/7 activity in the mammosphere. Low expression of miR-6844 decreased migratory and invasive cells by altering the expression of Snail, E-cad, and Vimentin at mRNA/protein levels. In conclusion, loss of miR-6844 decreases stemness/self-renewal and other cancer hallmark in breast cancer stem-like cells through CD44-JAK2-STAT3 axis. Thus, downregulation of miR-6844 by therapeutic agents might be a novel strategy to target breast cancer stemness and self-renewal. � 2023 Wiley Periodicals LLC.Item Implications of vitamin D deficiency in systemic inflammation and cardiovascular health(Taylor and Francis Ltd., 2023-06-24T00:00:00) Dey, Sanjay Kumar; Kumar, Shashank; Rani, Diksha; Maurya, Shashank Kumar; Banerjee, Pratibha; Verma, Madhur; Senapati, SabyasachiClinical, epidemiological, and molecular studies have sufficiently highlighted the vitality of vitamin D [25(OH)D and 1,25(OH)2D] in human health and wellbeing. Globally, vitamin D deficiency (VDD) has become a public health concern among all age groups. There is a very high prevalence of VDD per the estimates from several epidemiological studies on different ethnic populations. But, population-specific scales do not support these estimates to define VDD clinically and consistent genetic associations. However, clinical studies have shown the relevance of serum vitamin D screening and oral supplementation in improving health conditions, pointing toward a more prominent role of vitamin D in health and wellness. Routinely, the serum concentration of vitamin D is measured to determine the deficiency and is correlated with physiological conditions and clinical symptoms. Recent research points toward a more inclusive role of vitamin D in different disease pathologies and is not just limited to otherwise bone health and overall growth. VDD contributes to the natural history of systemic ailments, including cardiovascular and systemic immune diseases. Considering its significant impact on premature morbidity and mortality, there is a compelling need to comprehensively review and document the direct and indirect implications of VDD in immune system deregulation, systemic inflammatory conditions, and cardio-metabolism. The recommendations from this review call for furthering our research concerning vitamin D and its direct and indirect implications. � 2023 Taylor & Francis Group, LLC.Item Mycobacterium Tubercular Mediated Inflammation and Lung Carcinogenesis: Connecting Links(LIDSEN Publishing Inc, 2023-06-21T00:00:00) Vashishth, Abhay; Shuaib, Mohd; Bansal, Tanya; Kumar, ShashankLung cancer is a leading cause of death among all the cancer worldwide and it has the highest occurrence and mortality rates. Mycobacterium tuberculosis (MTB) induced tuberculosis has been known as one of the risk factors for lung carcinogenesis. The exact mechanism of MTB is understood to date. Several research and epidemiological studies about the link between tuberculosis and lung cancer exist. It has been proposed that tuberculosis causes chronic inflammation, which increases the risk of lung cancer by creating a favorable environment. EGFR downstream signaling promotes constitutive activation of TKIs domain due to the mutation in exon 19 and exon 21 (L858R point mutation), which leads to cell proliferation, invasion, metastasis, and angiogenesis, causing lung adenocarcinoma. Several other studies have shown that human monocyte cells infected by MTB enhance the invasion and cause induction of epithelial-mesenchymal transition (EMT) characteristics in lung cancer cell co-culture. This review article has tried to draw a relationship between chronic tuberculosis and lung carcinogenesis. � 2023 by the author.Item Anti-proliferative, apoptosis inducing, and antioxidant potential of Callistemon lanceolatus bark extracts: an in vitro and in silico study(Springer, 2023-05-08T00:00:00) Kumar, Ramesh; Kushwaha, Prem Prakash; Singh, Atul Kumar; Kumar, Shashank; Pandey, Abhay KumarThe present study reports anticancer and antioxidant activities of Callistemon lanceolatus bark extracts. Anticancer activity was studied against MDA-MB-231 cells. Antioxidant assessment of the chloroform and methanol extracts showed considerable free radical scavenging, metal ion chelating, and reducing power potential. Chloroform extract exhibited potent inhibition of cancer cell proliferation in MTT assay (IC50 9.6�?g/ml) and promoted programmed cell death. Reactive oxygen species (ROS) generation, mitochondria membrane potential (MMP) disruption ability, and nuclear morphology changes were studied using H2-DCFDA, JC-1, and Hoechst dyes, respectively, using confocal microscopy. Apoptotic cells exhibited fragmented nuclei, increased ROS generation, and altered MMP in dose- and time-dependent manner. Chloroform extract upregulated the BAX-1 and CASP3 mRNA expression coupled with downregulation of BCL-2 gene. Further, in silico docking of phytochemicals present in C. lanceolatus with anti-apoptotic Bcl-2 protein endorsed apoptosis by its inhibition and thus corroborated the experimental findings. Obatoclax, a known inhibitor of Bcl-2 was used as a reference compounds. � 2023, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.Item GNL3 and PA2G4 as Prognostic Biomarkers in Prostate Cancer(MDPI, 2023-05-12T00:00:00) Kumar, Shashank; Shuaib, Mohd; AlAsmari, Abdullah F.; Alqahtani, Faleh; Gupta, SanjayProstate cancer is a multifocal and heterogeneous disease common in males and remains the fifth leading cause of cancer-related deaths worldwide. The prognosis of prostate cancer is variable and based on the degree of cancer and its stage at the time of diagnosis. Existing biomarkers for the prognosis of prostate cancer are unreliable and lacks specificity and sensitivity in guiding clinical decision. There is need to search for novel biomarkers having prognostic and predictive capabilities in guiding clinical outcomes. Using a bioinformatics approach, we predicted GNL3 and PA2G4 as biomarkers of prognostic significance in prostate cancer. A progressive increase in the expression of GNL3 and PA2G4 was observed during cancer progression having significant association with poor survival in prostate cancer patients. The Receiver Operating Characteristics of both genes showed improved area under the curve against sensitivity versus specificity in the pooled samples from three different GSE datasets. Overall, our analysis predicted GNL3 and PA2G4 as prognostic biomarkers of clinical significance in prostate cancer. � 2023 by the authors.