The accurate prediction of ligand-protein binding free energies is crucial in hit identification and hit-to-lead optimization. In Binary Star, we run rigorous absolute binding free energy calculations using different protocols such as the alchemical free energy perturbation (FEP) method and the geometrical approach using the adaptive biasing force (ABF) method. We also perform end-point relative binding free energy calculations using various protocols such as molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) and molecular mechanics generalized Born surface area (MM/GBSA) and relative-FEP methods. https://lnkd.in/g–nrnzw

Undiscovered Potential of Minor Cannabinoids The enormous therapeutic potential of minor cannabinoids is due to their interaction with central nervous system (CNS) receptors. The effects of various cannabinoids vary depending on the receptors to which they bind. Depending on the nature of their interaction, structural biology and computational chemistry could combine to offer mechanistic insight into the following categories of minor cannabinoids interacting with GPCR: antagonists, partial agonists, inverse agonists, and agonists. In-Silico research on cannabinoids has grown significantly, and it is anticipated to move forward quickly as more GPCR structures are solved.

Drug repurposing is an effective strategy in discovering or developing drug molecules with new pharmacological/therapeutic indications. In recent years, many pharmaceutical companies are developing new drugs with the discovery of novel biological targets by applying the drug repositioning strategy in drug discovery and development program. It utilizes the combined efforts of activity-based or experimental and in silico-based or computational approaches to develop/identify the new uses of drug molecules on a rational basis. This highly efficient, time saving, low-cost strategy maximizes the therapeutic value of a drug to combat particularly, rare, difficult-to-treat diseases and neglected diseases.

RNA based therapeutics is gaining rapid attention, since it provides an excellent opportunity for the development of drugs that target pathways involving \”undruggable\” proteins. This rapidly expanding field offers exciting possibilities for applying structure-based drug design strategies to come up with viable solutions. In this context, computational modelling can provide interesting leads for speeding up the RNA based drug discovery process. At Binary Star, we offer computational solutions to this challenging problem, using a large database of small molecules that have properties specific for binding RNA. https://lnkd.in/gYycxJuH

Drug Discovery and Development is long, risky, and expensive road (it takes ~ 8 years long and ~ 2 billion cost). Any tactic that may help to reduce the high capitalized costs is expected to significantly improve the productivity of drug discovery efforts to bring novel and more effective small-molecule drug therapies to the clinic. Computer-aided drug design (CADD) is crucial in the contemporary drug development pipeline. In the Binary Star, we use cutting-edge computational tools to foster and accelerate drug discovery campaigns. Our platform facilitates the discovery of novel molecules with a higher hit rate of success compared to traditional methods.

Let’s discuss how we can find a solution to your complex queries: The mechanism of action of drugs and probes Development Strategies for the partnership\’s objectives and potential outcomes and impacts. Describe the novel ideas or approaches required to address the issue and how the research would fill knowledge gaps. Comprehension of molecular and structural biology, as well as mechanisms of action and side effects explore the fundamentals of the interaction of drugs or small molecules with their targets, and even specific identification of molecular targets Computational defines the workflow for each project\’s evaluation and validation of the drug design. We offer expertise and in-depth knowledge in computational modeling of protein-ligand interactions to investigate the molecular biology and mechanisms of action of particular molecules being investigated as therapeutics, design new pharmaceutical agents, and create new probes to better comprehend biological mechanisms. https://www.mdpi.com/1424-8247/15/2/222

The emergence of antibiotic resistance in bacteria is a serious threat to the public health worldwide. Riboswitches are RNA-based targets that can help produce novel antibiotics via an innovative mechanism of action not applicable for proteins. Since no bacterial riboswitch analogues exist in human genomic transcripts, it is possible to rationally design potent structural or functional analogues of the natural ligands of riboswitches, that can be exploited to starve bacterial cells of essential metabolites. We, at the Binary Star, are utilizing a robust computational pipeline to initiate a drug discovery program for the development of antibacterials that target specific bacterial riboswitches, using a large dataset of carefully selected ligands from the Binary Star database (BDS), that have properties specific to RNA binding.

Binary Star Database (BSD) is a carefully curated library of drug-like molecules. BSD was preprocessed and filtered using in-house scripts to remove unfavorite molecules. These molecules have good ADME properties, free of Pan-Assay Interference compounds (PAINS), and free of unwanted functionalities. The library is available as smiles as well as 3D ready-to-dock SDF format. By leveraging BSD, we can run high-throughput virtual screening using ligand-based and structure-based approaches for a target of interest. BSD also can be steered to match certain needs of different drug discovery projects. Stay tuned, more is coming!!