Computational Biology and Chemistry This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.

Computational analysis of substrate recognition of Sars-Cov-2 Mpro main protease
Comput Biol Chem. 2023 Sep 20;107:107960. doi: 10.1016/j.compbiolchem.2023.107960. Online ahead of print.ABSTRACTMpro main protease takes an essential role in the Sars-Cov-2 viral life cycle by releasing the individual protein from the single poly-peptide chain via proteolytic cleavage in the beginning of the viral infection. Interfering with this step by inhibiting the protease with small compound-based inhibitors has been proven to be an effective strategy to treat the infection. Thus, understanding the substrate recognition mechanism of the Mpro main protease has gained great interest from the beginning of the pandemic....
Source: Computational Biology and Chemistry - September 24, 2023 Category: Bioinformatics Authors: Hilal Sena Tasci Ebru Akkus Muslum Yildiz Abdulkadir Kocak Source Type: research

Assessment of the hypoglycemic and anti-hemostasis effects of Paederia foetida (L.) in controlling diabetes and thrombophilia combining in vivo and computational analysis
Comput Biol Chem. 2023 Sep 9;107:107954. doi: 10.1016/j.compbiolchem.2023.107954. Online ahead of print.ABSTRACTPaederia foetida is valued for its folk medicinal properties. This research aimed to assess the acute toxicity, hypoglycemic and anti-hemostasis properties of the methanolic extract of P. foetida leaves (PFLE). Acute toxicity of PFLE was performed on a mice model. Hypoglycemic and anti-hemostasis properties of PFLE were investigated on normal and streptozotocin-induced mice models. Deep learning, molecular docking, density functional theory, and molecular simulation techniques were employed to understand the unde...
Source: Computational Biology and Chemistry - September 22, 2023 Category: Bioinformatics Authors: Jannatul Ferdous Md Ekhtiar Rahman Farzana Sayed Sraboni Amit Kumar Dutta Md Siddikur Rahman Md Roushan Ali Biswanath Sikdar Alam Khan Md Faruk Hasan Source Type: research

Graph Attention Network based mapping of knowledge relations between chemical spaces of Nuclear factor kappa B and Centella asiatica
This study aims to explore the regulatory nature of the molecules from the inhibition and activation of the NF-κB bioassay data set and map this information for a knowledge-based analysis against the molecules of CA, a low-growing tropical plant. This finding has led to a new direction in the field, transitioning from the conventional active-inactive framework to a more comprehensive active-inactive-regulatory model. This approach can be thoroughly explored by leveraging a graph-based deep learning system. The study presents an innovative approach using a Graph Attention Network (GAT) to rank CA molecules in chemical spac...
Source: Computational Biology and Chemistry - September 21, 2023 Category: Bioinformatics Authors: Vivek P Mithun Mohanan Shajil U K Sandesh E Pa Jaleel U C A Source Type: research

The marijuana-schizophrenia multifaceted nexus: Connections and conundrums towards neurophysiology
Comput Biol Chem. 2023 Sep 12;107:107957. doi: 10.1016/j.compbiolchem.2023.107957. Online ahead of print.ABSTRACTDelta-9-tetrahydrocannabinol, a component of marijuana, interacts with cannabinoid receptors in brain involved in memory, cognition, and emotional control. However, marijuana use and schizophrenia development is a complicated and contentious topic. As a result, more investigation is needed to understand this relationship. Through the functional enrichment analysis, we report the delta-9-tetrahydrocannabinol to manipulate the homeostatic biological process and molecular function of different macromolecules. Addit...
Source: Computational Biology and Chemistry - September 20, 2023 Category: Bioinformatics Authors: Pukar Khanal Vishal S Patil B M Patil Kunal Bhattacharya Amit Kumar Shrivastava Raushan K Chaudhary Lokjan Singh Prarambh Sr Dwivedi Darasaguppe R Harish Subarna Roy Source Type: research

Quantum gate algorithm for reference-guided DNA sequence alignment
We present a novel quantum algorithm for reference-guided DNA sequence alignment modeled with gate-based quantum computing. The algorithm is scalable, can be integrated into existing classical DNA sequencing systems and is intentionally structured to limit computational errors. The quantum algorithm has been tested using the quantum processing units and simulators provided by IBM Quantum, and its correctness has been confirmed.PMID:37717360 | DOI:10.1016/j.compbiolchem.2023.107959 (Source: Computational Biology and Chemistry)
Source: Computational Biology and Chemistry - September 17, 2023 Category: Bioinformatics Authors: G D Varsamis I G Karafyllidis K M Gilkes U Arranz R Martin-Cuevas G Calleja P Dimitrakis P Kolovos R Sandaltzopoulos H C Jessen J Wong Source Type: research

New thiazolidine-2,4-diones as effective anti-proliferative and anti-VEGFR-2 agents: Design, synthesis, in vitro, docking, MD simulations, DFT, ADMET, and toxicity studies
Comput Biol Chem. 2023 Sep 11;107:107958. doi: 10.1016/j.compbiolchem.2023.107958. Online ahead of print.ABSTRACTNovel thiazolidine-2,4-dione derivatives, 11a-g, were designed, and synthesized targeting the VEGFR-2 protein. The in vitro studies indicated the abilities of the synthesized derivatives to inhibit VEGFR-2 and prevent the growth of two different cancer cell types, HepG2 and MCF-7. Compound 11 f exhibited the strongest anti-VEGFR-2 activity (IC50 = 0.053 µM). As well, compound 11 f showed impressive anti-proliferative activity against the mentioned cancer cell lines with IC50 values of 0.64 ± 0.01 and 0.53 ± 0...
Source: Computational Biology and Chemistry - September 15, 2023 Category: Bioinformatics Authors: Hazem Elkady Abdelrahman A Abuelkhir Mahmoud Rashed Mohammed S Taghour Mohammed A Dahab Hazem A Mahdy Alaa Elwan Hanan A Al-Ghulikah Eslam B Elkaeed Ibrahim M Ibrahim Dalal Z Husein Ahmed Metwaly Ibrahim H Eissa Source Type: research

Design, semi-synthesis, anti-cancer assessment, docking, MD simulation, and DFT studies of novel theobromine-based derivatives as VEGFR-2 inhibitors and apoptosis inducers
In conclusion, our in vitro and in silico investigations showed that compound 15 exhibited promising apoptotic anticancer potential through the suppression of VEGFR-2.PMID:37673011 | DOI:10.1016/j.compbiolchem.2023.107953 (Source: Computational Biology and Chemistry)
Source: Computational Biology and Chemistry - September 6, 2023 Category: Bioinformatics Authors: Ibrahim H Eissa Reda G Yousef Hazem Elkady Eslam B Elkaeed Aisha A Alsfouk Dalal Z Husein Ibrahim M Ibrahim Mostafa A Elhendawy Murrell Godfrey Ahmed M Metwaly Source Type: research

Multilayer precision-based screening of potential inhibitors targeting Mycobacterium tuberculosis acetate kinase using in silico approaches
Comput Biol Chem. 2023 Aug 23;107:107942. doi: 10.1016/j.compbiolchem.2023.107942. Online ahead of print.ABSTRACTTuberculosis (TB), caused by Mycobacterium tuberculosis (MTB), remains a major threat to global health, with the emergence of multi-drug and extensively drug-resistant strains posing a serious challenge. Thereby, understanding the molecular basis of MTB virulence and disease pathogenesis is critical for developing effective therapeutic strategies. Targeting proteins involved in central metabolism has been recognized as a promising therapeutic approach to combat MTB. In this regard, the enzyme AckA of the acetate...
Source: Computational Biology and Chemistry - September 6, 2023 Category: Bioinformatics Authors: Sneha Subramaniyan Hemavathy Nagarajan Umashankar Vetrivel Jeyakanthan Jeyaraman Source Type: research