Advancing RNA Targeting with Computational Technologies at Binary Star

The perspective article of Bernetti et al. (vide infra) discusses expected properties of RNA binding ligands and throws light on the recognition of RNA by small molecule binders. We, at Binary Star Research Services are also heavily involved in applications of cutting edge computational technologies to target structured RNA using small molecules. https://lnkd.in/gfdbzjnc

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Analyzing Guanidinium Salt Interactions with Proteins: Insights into Binding and Denaturation

Our computational work on the interaction of Guanidinium salts with proteins is now available on PCCP’s website. This work will help better understand protein ligand binding and protein denaturation processes. In the present work, 86 available high resolution X-ray structures of proteins that contain one or more guanidinium ions (Gdm+) are analyzed for the distribution and nature of noncovalent interactions between Gdm+ and amino-acid residues. A total of 1044 hydrogen-bonding interactions were identified, of which 1039 are N–H⋯O, and five are N–H⋯N. Acidic amino acids are more likely to interact with Gdm+ (46% of interactions, 26% Asp and 20% Glu), followed by Pro (19% of interactions). DFT calculations on the identified Gdm+–amino acid hydrogen-bonded pairs reveal that although Gdm+ interacts primarily with the backbone amides of nonpolar amino acids, Gdm+ does interact with the sidechains of polar and acidic amino acids. We classified the optimized Gdm+–amino acid pairs into parallel [p], bifurcated [b], single hydrogen bonded [s] and triple hydrogen bonded [t] types. The [p] and [t] type pairs possess higher average interaction strength that is stronger than that of [b] and [s] type pairs. Negatively charged aspartate and glutamate residues interact with Gdm+ ion exceptionally tightly (−76 kcal mol−1) in [p] type complexes. This work provides statistical and energetics insights to better describe the observed destabilization or denaturation process of proteins by guanidinium salts. https://doi.org/10.1039/D2CP04943K

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Overcoming Undruggable Targets: Innovative Approaches in Drug Discovery

#Targeting Undruggable Targets Thousand or fewer proteins have been claimed as potentially therapeutic, despite the fact that the human genome can encode more than 20,000 different proteins. Undruggable targets have the following specified characteristics: extended and shallow binding pockets or even no pocket, and lack of specific ligands that perform critical effects, In contrast to the goal of inhibition, drugs must restore protein activity, which is more complicated. The leading process of drug discovery is targeting undruggable targets. novel pharmaceutical entities, such as bifunctional compounds, covalent drugs, peptide-based drugs, protein-based drugs, and RNA therapeutics, have been designed to overcome undruggable barriers. In BinaryStar we perform merging computer-aided drug design multiple approaches such as DNA-encoded libraries, Nucleic Acid-Base Drug Design, Targeting DNA/RNA, Fragment-Based Virtual Screening, Allosteric Site exploring, and all drug discovery techniques to dealing with more ‘undruggable’ targets in the future.  www.tandfonline.com 

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Computer-Aided Drug Discovery Market Set to Reach $7.5 Billion by 2030

Global Computer-aided Drug Discovery Market Reach $7.5 Billion by 2030 at a CAGR of 11.48% the severe coronavirus virus (COVID-19), the cardiovascular disease sub-segment, the rapidly growing occurrence of diabetes and cancer, the sub-segment for structure-based drug design, increasing frequency of chronic and undiagnosed diseases, and Oncology are expected to drive the market for computer-aided drug discovery during the following decade. Due to growing R&D efforts by scientists, researchers, and biotech and pharmaceutical companies, the market for CADD has been predicted to experience rapid Growth. https://lnkd.in/faVEqE5

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Exploring Extra-Tissue GPCRs: Novel Targets Beyond Smell and Taste

The expression of GPCRs that detect smell and taste has traditionally been thought to be tissue specific. However, studies over the past two decades strongly suggest that these receptors are expressed in many other tissues in the body, and can be potential drug targets. However, studies on structure-activity relationships of olfactory and taste receptors have been hampered due to scarce structural information and inadequate sequence similarities with the well resolved GPCR classes. Our Binary Star Research Team has been deeply involved in developing reliable models and utilizing the associated structural information for the development of novel scaffolds that target extra-oral and extra-olfactory taste and olfactory GPCRs. https://lnkd.in/e_hMagWq

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