791 search results for “bioactive molecules” in the Public website
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Innovative strategies to clinically characterize the human tear proteome
Transplantation of labial salivary glands to the eyelids for patients with dry eye appears to give excellent results clinically.
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Rapid and profound rewiring of brain lipid signaling networks by acute diacylglycerol lipase inhibition
Diacylglycerol lipases (DAGLα and DAGLβ) convert diacylglycerol to the endocannabinoid 2-arachidonoylglycerol. Our understanding of DAGL function has been hindered by a lack of chemical probes that can perturb these enzymes in vivo.
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Key publications
Key publications of the Computational Drug Discovery group
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Michel Orrit receives Spinoza Prize in Royal Theatre
On September 12, Michel Orrit received his Spinoza prize in the Royal Theatre in The Hague from OCW Secretary of State Sander Dekker. With the award comes a budget of 2.5 million euro, to be spent freely on scientific research, and the coveted Spinoza statue. Orrit shared the honor with Eveline Crone…
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Michel Orrit wins Physica Prize 2016
Michel Orrit was awarded the Physica prize 2016 for his groundbreaking work on single molecule spectroscopy.
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Uncovering the ingredients for planet formation
This thesis discusses the physical and chemical processes than influence the composition of forming planets.
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PhD Theses
A full overview of THEOR PhD theses.
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Physicist Michel Orrit new member KNAW
The Royal Netherlands Academy of Arts and Sciences (KNAW) selects prominent researchers as members based on their scientific achievements. On September 17th, the KNAW will install 21 new members, including Leiden physicist Michel Orrit.
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Chemistry between stars and planets
In the large gas clouds between the stars, chemical reactions take place under extreme conditions, giving rise to both small molecules, such as water and common salt, as well as large complex molecules that can serve as the building blocks of life. This is known as astrochemistry and it is something…
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Michel Orrit and Hermen Overkleeft members KNAW
The Royal Netherlands Academy of Arts and Sciences (KNAW) selects prominent researchers as members based on their scientific achievements. On September 17th, the KNAW will install 21 new members, including Leiden physicist Michel Orrit and chemist Hermen Overkleeft.
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Affinity-based profiling of the adenosine receptors
The adenosine receptors are proteins that reside in the extracellular membranes of cells. Activation of adenosine receptors plays a role in many physiological and pathological processes, such as immune responses and cancers.
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New generation of graphene biosensors based on smooth surfaces and sharp edges
The surface and the edges of graphene are expected to provide higher sensitivity and specificity in detecting and characterizing single molecules. However fundamental physical limits exist in reaching an ultimate precision in detecting the dynamics of chemical and biological systems. The research in…
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To explore the drug space smarter: Artificial intelligence in drug design for G protein-coupled receptors
Over several decades, a variety of computational methods for drug discovery have been proposed and applied in practice. With the accumulation of data and the development of machine learning methods, computational drug design methods have gradually shifted to a new paradigm, i.e. deep learning methods…
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Reactivity on interstellar ice analogues
The
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Research
Research at the THEOR group is comprised of the following research themes:
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Elucidating the catalytic properties of gold
How does CO adsorption on gold promote its own oxidation and the oxidation of other organic molecules?
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Research
Developing computational algorithms for structural biology -A high resolution, three dimensional view of a molecule provides detailed information that help elucidate its function: by knowing the exact arrangement of atoms in a molecule, we can understand disease, develop drugs to combat them and improve…
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Laboratory studies of Water Ice in Space
Astronomical observations of cold regions in the universe show a rich inventory of ices. Part of these ices may end up on planets like our own, but in that journey they will be exposed to considerable amounts of radiation.
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Data mining and algorithm development
Due to the modern techniques of combinatorial chemistry and high-throughput screening, data on the biological activity of many millions of compounds is known. However, it is still very difficult to transfer this data into knowledge: if we know that compounds A and B bind to a certain protein with high…
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NWO grants two IBL-proposals by interdisciplinary research consortia
Recently, NWO has decided to grant two interdisciplinary research proposals for national and international consortia submitted by researchers from the Institute of Biology Leiden. One of the proposals is led by Prof. dr. Ariane Briegel, the other one by dr. Remko Offringa.
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Research lines
Physics and Engineering Approaches to Biomedicine and Pharmacology
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Physics and Engineering Approaches to Biomedicine and Pharmacology
Mashaghi lab conducts research at the interface of physics, engineering and biomedicine. We develop and use theoretical and experimental approaches to address basic and applied research problems.
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Gas-surface reaction dynamics and surface science
The local ordering of atoms at the surface of a metallic particle determines its catalytic activity and selectivity. As energy systems of the future will be based on efficient catalytic conversion of small molecules in closed cycles, we study how structural effects of catalysts can be used to our ad…
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Novel target engagement biomarkers for better drug candidates
Is is possible to better predict the validity of drug candidates?
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Novel chemical tools for target validation in neuroinflammation
In what way can new tools and techniques be used to develop drug candidates for the treatment of neurological disorders?
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Non-equilibrium chemistry and cooling in simulations of galaxy formation
Promotor: J. Schaye
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Highly Efficient Activation of HCl Dissociation on Au(111) via Rotational Preexcitation
The probability for dissociation of molecules on metal surfaces, which often controls the rate of industrially important catalytic processes, can depend strongly on how energy is partitioned in the incident molecule. There are many example systems where the addition of vibrational energy promotes reaction…
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1,2-cis-glycosylations: method development and synthesis of complex oligosaccharides
Promotor: G.A. van der Marel, Co-promotor: D.C. Codée
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A new method to reconstruct the structure from crystal images
Promotor: J.P. Abrahams, Co-promotor: T. Grüne
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Amin Moradi
Science
moradi@physics.leidenuniv.nl | +31 71 527 5676
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Fatema Zahra Rashid
Science
f.z.m.rashid@lic.leidenuniv.nl | +31 71 527 1037
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Mycobacterial dihydrofolate reductase inhibitors identified using chemogenomic methods and in vitro validation
Source: PLoS ONE, Volume 10, Issue 3 (2015)
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Hortus botanicus
Hidden behind the Academy Building on the Rapenburg lies the oldest botanical garden of the Netherlands and one of the oldest gardens in the world. Founded in 1590 and expanded in the following centuries, the Hortus is the green heart of Leiden.
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Dynamic hydrogels as synthetic extracellular matrices for three- dimensional cell culture
Synthetic hydrogels that mimic the natural extracellular matrix in the biophysical and biochemical cues it provides to cells are in high demand, however the cell phenotypes as they are observed in vivo in numerous cases have yet to be attained.
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Dissociative chemisorption on transition metal surfaces
The dissociative chemisorption of a molecule on a transition metal surface represents a rate-limiting step in many heterogeneously catalyzed processes, whereby most chemicals are made. In spite of the importance of this reaction, an accurate first principles approach to modeling it does not yet exist.…
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Chemical Probe Facility
The Chemical Probe Facility is part of the Leiden Early Drug Discovery & Development (LED3) center. Activity-based protein profiling (ABPP) is one of the pillars of chemical biology. ABPP determines the activity of entire protein families in living cells and tissues under physiological conditions, such…
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LED3 Lecture: Natural Product Antibiotics: Past, Present, Future
Lecture
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The immune system in action against cervical cancer
In the hunt for a vaccine against cervical cancer, fundamental knowledge about the immune system and organic chemistry have been brought together and have already resulted in a vaccine that is now being tested in clinical trials. Scientists are now working hard on an improved variant.
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Flagships
In CCLS several subgroups have formed, below you can find an overview of these groups with the names of the leading researchers and a short outline of the project.
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Surface Reactivity of Activated CO2 Selective use of energy in splitting CO2
Juurlink
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C.J. Kok Jury Award for Thesis of the Year
Isotopes on exoplanets, a more efficient memory for data centres or new molecules that work against the Zika virus and HIV. Which PhD candidate has written the most impressive dissertation of 2023? The jury of the C.J. Kok Jury Award faces the challenging task of deciding that. Meet the nominees of…
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Mechanism-based inhibitors and probes for neuraminidases
Neuraminidases are enzymes that cleave glycosidic linkages of sialic acid. These enzymes are involved in influenza infections as well as in many cellular processes in mammals and micro-organisms.
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Accurate modeling of the dynamics of dissociative chemisorption on metal surfaces
Fundamental understanding of molecular reactions on metal surfaces is important for improving heterogeneous catalysis.
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Stefan Semrau Lab - Quantitative Single-Cell Biology
We study cell-fate decision-making using embryonic stem cells as a model system. Stem cells integrate a large number of cues to direct their development into a great variety of cell types.
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Chemically Accurate Simulation of a Prototypical Surface Reaction: H-2 Dissociation on Cu(111)
Methods for accurately computing the interaction of molecules with metal surfaces are critical to understanding and thereby improving heterogeneous catalysis.
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Structure dependence of molecular reactions on surfaces
The research presented in this thesis makes use of small molecules (as H2 , D2 and O2 ) on well-defined single crystal surfaces (flat Pt(111), flat Cu(211) and curved Pt(111)) to elucidate the role of surface structure and degrees of freedom in the reactant in specific surface reactions.
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Vaccination and Targeted Therapy Using Liposomes; Opportunities for Treatment of Atherosclerosis and Cancer
This thesis focuses on using liposomes in two different treatment strategies; vaccination (or immunotherapy) and delivery of a small molecule, and in two different disease models; cancer and atherosclerosis.
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Structure-affinity relationships (SARs) and structure-kinetics relationships (SKRs) of Kv11.1 blockers
Source: J Med Chem (2015)
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NMR Facility
Nuclear Magnetic Resonance (NMR) Spectroscopy is a non-destructive analytical technique that is used to study the nature and characteristics of molecules with an atomic level precision. It has a wide range of applications especially in synthetic chemistry, biological and biochemical research groups…
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Computational approaches to dissociative chemisorption on metals: towards chemical accuracy
We review the state-of-the-art in the theory of dissociative chemisorption (DC) of small gas phase molecules on metal surfaces, which is important to modeling heterogeneous catalysis for practical reasons, and for achieving an understanding of the wealth of experimental information that exists for this…