Random Peptide Library for Ligand and Drug Discovery

Kubo, Tai

doi:10.1007/978-94-007-6452-1_2

Cited by 5 publications

(2 citation statements)

References 65 publications

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“…Yet, over the past decades, a paradigm shift from implementation of chemically derived drugs towards treatment with biological compounds (such as proteins, peptides or nucleic acids; Table 1 ) has occurred leading to a prominent and rapid expansion of the biopharmaceutical market [5] , [6] . The use of synthetic drugs is commonly associated with toxicity concerns due to their broad chemical reactivity with organic molecules [7] , while biologicals show fewer or no off-target activity due to higher specificity for their targets [8] , [9] . Today, the vast majority of commercially approved biologicals includes recombinant proteins, which are prevalently utilized as therapeutic antigens or antibodies for treatment of cancer, inflammatory or infectious diseases [4] , [10] .…”

Section: Introductionmentioning

confidence: 99%

mRNA – A game changer in regenerative medicine, cell-based therapy and reprogramming strategies

Chabanovska

Galow

Dávid

et al. 2021

Advanced Drug Delivery Reviews

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Section: Introductionmentioning

confidence: 99%

mRNA – A game changer in regenerative medicine, cell-based therapy and reprogramming strategies

Chabanovska

Galow

Dávid

et al. 2021

Advanced Drug Delivery Reviews

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“…Unquestionably, the most accurate way for 8 discovering effective ligand molecules, is experimental screening of various ligand 9 PLOS 2/7 candidates. Nevertheless, although robotic methods have facilitated carrying out 10 thousands of tests in one day [2][3][4], and several libraries of ligands have been compiled 11 and used [5][6][7], to this date, only a tiny portion of innumerable possibilities has been 12 screened [8]. Fortunately, the emergence of virtual screening [9][10][11] has provided a 13 cost-effective tool for exploring the ligand libraries.…”

mentioning

confidence: 99%

A Novel analog approach for fast evaluation of affinity between ligand and receptor in scaled up molecular models

Tavousi

Shahbazmohamadi

2018

Preprint

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Rational structure based drug design aims at identifying ligand molecules that bind to the active site of a target molecule with high affinity (low binding free energy), to promote or inhibit certain biofunctions. Thus, it is absolutely essential that one can evaluate such affinity for the predicted molecular complexes in order to design drugs effectively. A key observation is that, binding affinity is proportional to the geometric fit between the two molecules. Having a way to assess the quality of the fit enables one to rank the quality of potential drug solutions. Other than experimental methods that are associated with excessive time, labor and cost, several in silico methods have been developed in this regard. However, a main challenge of any computation-based method is that, no matter how efficient the technique is, the trade-off between accuracy and speed is inevitable. Therefore, given today's existing computational power, one or both is often compromised. In this paper, we propose a novel analog approach, to address the aforementioned limitation of computation-based algorithms by simply taking advantage of Kirchhoff's circuit laws. Ligand and receptor are represented with 3D printed molecular models that account for the flexibility of the ligand. Upon the contact between the ligand and the receptor, an electrical current will be produced that is proportional to the number of representative contact points between the two scaled up molecular models. The affinity between the two molecules is then assessed by identifying the number of representative contact points obtainable from the measured total electrical current. The simple yet accurate proposed technique, in combination with our previously developed model, Assemble-And-Match, can be a breakthrough in development of tools for drug design. Furthermore, the proposed technique can be more broadly practiced in any application that involves assessing the quality of geometric match between two physical objects. Introduction 1Rational structure-based drug design is the process of searching for molecules so called 2 as ligands that can geometrically fill the binding site of another molecule so called as 3 the receptor, with the purpose of activating or inhibiting some type of biofunction, 4 similarly to finding the right key for a lock [1]. Importantly, the affinity between the 5 selected ligand and the receptor of interest must be high compared to the potential 6 ligand competitors. In fact, this affinity reflects how favorable the bind between ligand 7 and the receptor is in terms of free energy. Unquestionably, the most accurate way for 8 discovering effective ligand molecules, is experimental screening of various ligand 9 PLOS 2/7 candidates. Nevertheless, although robotic methods have facilitated carrying out 10 thousands of tests in one day [2][3][4], and several libraries of ligands have been compiled 11 and used [5][6][7], to this date, only a tiny portion of innumerable possibilities has been 12 screened [8]. Fortunately, the emergence of virtual scree...

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Phage display and human disease detection

Kumari

Singh

et al. 2023

Progress in Molecular Biology and Translational Science

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Random Peptide Library for Ligand and Drug Discovery

Cited by 5 publications

References 65 publications

mRNA – A game changer in regenerative medicine, cell-based therapy and reprogramming strategies

mRNA – A game changer in regenerative medicine, cell-based therapy and reprogramming strategies

A Novel analog approach for fast evaluation of affinity between ligand and receptor in scaled up molecular models

Phage display and human disease detection

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