Influence of molecular shape on the retention of small molecules by solvent resistant nanofiltration (SRNF) membranes: A suitable molecular size parameter

2008 ◽  
Vol 318 (1-2) ◽  
pp. 114-122 ◽  
Author(s):  
Fengchun Zheng ◽  
Chunxi Li ◽  
Qipeng Yuan ◽  
Frank Vriesekoop
Keyword(s):  
Small Molecules ◽  
Molecular Size ◽  
Molecular Shape ◽  
Size Parameter

Medicinal Chemistry Database GDBMedChem

2019 ◽  
Author(s):  
Mahendra Awale ◽  
Finton Sirockin ◽  
Nikolaus Stiefl ◽  
Jean-Louis Reymond
Keyword(s):  
Small Molecules ◽  
Natural Product ◽  
Medicinal Chemistry ◽  
3D Visualization ◽  
Molecular Size ◽  
Similarity Searching ◽  
Complex Molecules ◽  
Synthetic Accessibility ◽  
Simple Chemical ◽  
Reduced Complexity

<div>The generated database GDB17 enumerates 166.4 billion possible molecules up to 17 atoms of C, N, O, S and halogens following simple chemical stability and synthetic feasibility rules, however medicinal chemistry criteria are not taken into account. Here we applied rules inspired by medicinal chemistry to exclude problematic functional groups and complex molecules from GDB17, and sampled the resulting subset evenly across molecular size, stereochemistry and polarity to form GDBMedChem as a compact collection of 10 million small molecules.</div><div><br></div><div>This collection has reduced complexity and better synthetic accessibility than the entire GDB17 but retains higher sp 3 - carbon fraction and natural product likeness scores compared to known drugs. GDBMedChem molecules are more diverse and very different from known molecules in terms of substructures and represent an unprecedented source of diversity for drug design. GDBMedChem is available for 3D-visualization, similarity searching and for download at http://gdb.unibe.ch.</div>

scholarly journals Correlations between retention volume and molecular size parameters in gel permeation chromatography of small molecules

1975 ◽  
Vol 28 (1) ◽  
pp. 189 ◽  
Author(s):  
RA Shanks
Keyword(s):  
Molecular Weight ◽  
Small Molecules ◽  
Organic Molecules ◽  
Retention Volume ◽  
Molecular Size ◽  
Gel Permeation Chromatography ◽  
Molar Volumes ◽  
Small Organic Molecules ◽  
Molecular Dimension ◽  
Gel Permeation

Gel permeation columns of Bio Beads S-X8 have been used to provide separation of oligomers and other small organic molecules. Results show successful separations up to molecular weight c. 600. The retention times of compounds have been correlated with the largest molecular dimension of the molecules and also with molar volumes.

scholarly journals Recent Advances in Application of Biosensors in Tissue Engineering

2014 ◽  
Vol 2014 ◽  
pp. 1-18 ◽  
Author(s):  
Anwarul Hasan ◽  
Md Nurunnabi ◽  
Mahboob Morshed ◽  
Arghya Paul ◽  
Alessandro Polini ◽  
...  
Keyword(s):  
Tissue Engineering ◽  
Cell Culture ◽  
Small Molecules ◽  
Real Time ◽  
Inflammatory Cytokines ◽  
Serum Proteins ◽  
Molecular Size ◽  
Medical Diagnostics ◽  
Alpha Fetoprotein ◽  
Pharmaceutical Industries

Biosensors research is a fast growing field in which tens of thousands of papers have been published over the years, and the industry is now worth billions of dollars. The biosensor products have found their applications in numerous industries including food and beverages, agricultural, environmental, medical diagnostics, and pharmaceutical industries and many more. Even though numerous biosensors have been developed for detection of proteins, peptides, enzymes, and numerous other biomolecules for diverse applications, their applications in tissue engineering have remained limited. In recent years, there has been a growing interest in application of novel biosensors in cell culture and tissue engineering, for example, real-time detection of small molecules such as glucose, lactose, and H2O2as well as serum proteins of large molecular size, such as albumin and alpha-fetoprotein, and inflammatory cytokines, such as IFN-g and TNF-α. In this review, we provide an overview of the recent advancements in biosensors for tissue engineering applications.

scholarly journals Equilibrium partitioning of macromolecules in confining geometries: Improved universality with a new molecular size parameter

2008 ◽  
Vol 128 (12) ◽  
pp. 124904 ◽  
Author(s):  
Yanwei Wang ◽  
Günther H. Peters ◽  
Flemming Y. Hansen ◽  
Ole Hassager
Keyword(s):  
Molecular Size ◽  
Size Parameter ◽  
Equilibrium Partitioning

scholarly journals Scope of 3D Shape-Based Approaches in Predicting the Macromolecular Targets of Structurally Complex Small Molecules Including Natural Products and Macrocyclic Ligands

2020 ◽  
Author(s):  
Ya Chen ◽  
Neann Mathai ◽  
Johannes Kirchmair
Keyword(s):  
Natural Products ◽  
Small Molecules ◽  
Knowledge Base ◽  
Target Prediction ◽  
Molecular Shape ◽  
Macrocyclic Compounds ◽  
Success Rates ◽  
Complex Molecules ◽  
Complete Failure ◽  
Prediction Approach

A plethora of similarity-based, network-based, machine learning and docking approaches for predicting the macromolecular targets of small molecules are available today and recognized as valuable tools for providing guidance in early drug discovery. With the increasing maturity of target prediction methods, researchers have started to explore ways to expand their scope to more challenging molecules such as structurally complex natural products and macrocyclic small molecules. In this work we systematically explore the capacity of an alignment-based approach to identify the targets of structurally complex small molecules (including large and flexible natural products and macrocyclic compounds) based on the similarity of their 3D molecular shape to non-complex molecules (i.e. more conventional, "drug-like", synthetic compounds). For this analysis, query sets of ten representative, structurally complex molecules were compiled for each of 35 pharmaceutically relevant proteins. Subsequently, ROCS, a leading shape-based screening engine, was utilized to generate rank-ordered lists of the potential targets of the 35x10 queries according to the similarity of their 3D molecular shape with that of compounds from a knowledge base of 272 640 non-complex small molecules active on a total of 3642 different proteins. Four of the scores implemented in ROCS were explored for target ranking, with the TanimotoCombo score consistently outperforming all others. The score successfully recovered the targets of 29% and 40% of the 350 queries among the top-5 and top-20 positions, respectively. For 29 out of the 35 investigated targets (83%), the method correctly assigned the first rank (out of 3642) to the target of interest for at least one of the ten queries. The shape-based target prediction approach showed remarkable robustness, with good success rates obtained even for compounds that are clearly distinct from any of the ligands present in the knowledge base. However, complex natural products and macrocyclic compounds proved to be challenging even with this approach, although cases of complete failure were recorded only for a small number of targets.

scholarly journals Total synthesis reveals atypical atropisomerism in a small-molecule natural product, tryptorubin A

Science ◽  
2020 ◽  
Vol 367 (6476) ◽  
pp. 458-463 ◽  
Author(s):  
Solomon H. Reisberg ◽  
Yang Gao ◽  
Allison S. Walker ◽  
Eric J. N. Helfrich ◽  
Jon Clardy ◽  
...  
Keyword(s):  
Total Synthesis ◽  
Small Molecules ◽  
Natural Product ◽  
Small Molecule ◽  
Molecular Shape ◽  
Molecular Graphs ◽  
Synthetic Strategy

Molecular shape defines function in both biological and material settings, and chemists have developed an ever-increasing vernacular to describe these shapes. Noncanonical atropisomers—shape-defined molecules that are formally topologically trivial but are interconvertible only by complex, nonphysical multibond torsions—form a unique subset of atropisomers that differ from both canonical atropisomers (e.g., binaphthyls) and topoisomers (i.e., molecules that have identical connectivity but nonidentical molecular graphs). Small molecules, in contrast to biomacromolecules, are not expected to exhibit such ambiguous shapes. Using total synthesis, we found that the peptidic alkaloid tryptorubin A can be one of two noncanonical atropisomers. We then devised a synthetic strategy that drives the atropospecific synthesis of a noncanonical atrop-defined small molecule.

Medicinal Chemistry Database GDBMedChem

2019 ◽  
Author(s):  
Mahendra Awale ◽  
Finton Sirockin ◽  
Nikolaus Stiefl ◽  
Jean-Louis Reymond
Keyword(s):  
Small Molecules ◽  
Natural Product ◽  
Medicinal Chemistry ◽  
3D Visualization ◽  
Molecular Size ◽  
Similarity Searching ◽  
Complex Molecules ◽  
Synthetic Accessibility ◽  
Simple Chemical ◽  
Reduced Complexity

<div>The generated database GDB17 enumerates 166.4 billion possible molecules up to 17 atoms of C, N, O, S and halogens following simple chemical stability and synthetic feasibility rules, however medicinal chemistry criteria are not taken into account. Here we applied rules inspired by medicinal chemistry to exclude problematic functional groups and complex molecules from GDB17, and sampled the resulting subset evenly across molecular size, stereochemistry and polarity to form GDBMedChem as a compact collection of 10 million small molecules.</div><div><br></div><div>This collection has reduced complexity and better synthetic accessibility than the entire GDB17 but retains higher sp 3 - carbon fraction and natural product likeness scores compared to known drugs. GDBMedChem molecules are more diverse and very different from known molecules in terms of substructures and represent an unprecedented source of diversity for drug design. GDBMedChem is available for 3D-visualization, similarity searching and for download at http://gdb.unibe.ch.</div>

Multiple scattering and the scattering of light by large or small molecules in solution

1965 ◽  
Vol 258 (1090) ◽  
pp. 387-420 ◽  
Keyword(s):  
Light Scattering ◽  
Small Molecules ◽  
Multiple Scattering ◽  
Additional Term ◽  
Molecular Size ◽  
Internal Field ◽  
Single Scattering ◽  
Particle Correlation ◽  
Molecular Weights ◽  
Two Component

The scattering equations for two-component fluids are formulated so that individual scattering processes take place in vacuo. A gauge transformation is made which transforms these processes to ones taking place in a medium of refractive index m. Certain previously controversial factors apparently associated with the internal field are thereby isolated and shown to be multiple scattering terms. The formulae for the scattered intensity and turbidity of a two-component fluid of small molecules are calculated by an entirely molecular argument; they agree with the forms usually quoted as Einstein’s formulae except that the additional term reported previously is confirmed. It is conjected that a very precise identity exists between the phenomenological and molecular treatments of scattering when multiple scattering is properly included. It is shown that the concept of an excess molecular polarizability in a two-component system of small molecules is valid only up to an approximation of single scattering: but the concept of excess scattering remains valid in the multiple scattering theory of such systems. It is also shown that without additional assumptions both these concepts cease to be valid even in the single scattering approximation when the solute molecules are large. These assumptions amount to a ‘uniform distribution’ (in a sense here specified) of the solvent round the solute in regions of radius of the order of iA: they can be interpreted as hydration (or solvation) conditions. From a crude model of a macromolecular solution it is suggested that the Debye corrections which derive from a finite molecular size to estimates of molecular weights determined by light scattering, could be in error by as much as 100% (~ 5% of molecular weights) or perhaps even more: estimates of molecular size by dissymmetry can also be in similar error. For a given solute, both these and the molecular weight corrections should vary from solvent to solvent. As this has not been reported experimentally, solutions of large molecules may satisfy the hydration conditions which are indeed shown to be both necessary and sufficient for the formal reduction of the scattering equations to Debye’s form. It may therefore, be possible to use light scattering to investigate the state of hydration of such molecules in a solvent and to investigate the three two-particle correlation functions of such systems.

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