Molecular and Cellular Modeling

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SEEK ID: https://publications.h-its.org/projects/10

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Project created: 7th Nov 2017

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Christina Athanasiou

Projects: Molecular and Cellular Modeling

Institutions: Heidelberg Institute for Theoretical Studies

https://orcid.org/0000-0003-2973-3550

Giulia D'Arrigo

Projects: Molecular and Cellular Modeling

Institutions: Heidelberg Institute for Theoretical Studies

Manuel Glaser

Projects: Molecular and Cellular Modeling

Institutions: Heidelberg Institute for Theoretical Studies

Xiaoming Hu

: inactive since 2021-06-13

Projects: Scientific Databases and Visualisation, Computational Molecular Evolution, Physics of Stellar Objects, Natural Language Processing, Molecular and Cellular Modeling, Molecular Biomechanics, Astroinformatics, Groups and Geometry, Playground, Computational Carbon Chemistry, Data Mining and Uncertainty Quantification, Computational Statistics

Institutions: Heidelberg Institute for Theoretical Studies, Heidelberg University

Goutam Mukherjee

Projects: Molecular and Cellular Modeling

Institutions: Heidelberg Institute for Theoretical Studies

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Heidelberg Institute for Theoretical Studies

Country: Germany

City: Heidelberg

Web page: https://www.h-its.org

An engineered variant of MECR reductase reveals indispensability of long-chain acyl-ACPs for mitochondrial respiration

Molecular and Cellular Modeling

Abstract (Expand)

Abstract Mitochondrial fatty acid synthesis (mtFAS) is essential for respiratory function. MtFAS generates the octanoic acid precursor for lipoic acid synthesis, but the role of longer fatty acid …

Authors: M. Tanvir Rahman, M. Kristian Koski, Joanna Panecka-Hofman, Werner Schmitz, Alexander J. Kastaniotis, Rebecca C. Wade, Rik K. Wierenga, J. Kalervo Hiltunen, Kaija J. Autio

Date Published: 1st Dec 2023

Publication Type: Journal

DOI: 10.1038/s41467-023-36358-7

Citation: Nat Commun 14(1),619

Created: 6th Feb 2023 at 09:30, Last updated: 6th Feb 2023 at 09:30

Multiscale molecular simulations to investigate adenylyl cyclase‐based signaling in the brain

Molecular and Cellular Modeling

Abstract

Not specified

Authors: Siri C. van Keulen, Juliette Martin, Francesco Colizzi, Elisa Frezza, Daniel Trpevski, Nuria Cirauqui Diaz, Pietro Vidossich, Ursula Rothlisberger, Jeanette Hellgren Kotaleski, Rebecca C. Wade, Paolo Carloni

Date Published: 2023

Publication Type: Journal

DOI: 10.1002/wcms.1623

Citation: WIREs Comput Mol Sci 13(1)

Created: 15th Jun 2022 at 08:24, Last updated: 27th Jan 2023 at 21:40

Brownian dynamics simulations of biomolecular diffusional association processes

Molecular and Cellular Modeling

Abstract

Not specified

Authors: Abraham Muñiz‐Chicharro, Lane W. Votapka, Rommie E. Amaro, Rebecca C. Wade

Date Published: 14th Dec 2022

Publication Type: Journal

DOI: 10.1002/wcms.1649

Citation: WIREs Comput Mol Sci

Created: 16th Dec 2022 at 12:24, Last updated: 27th Jan 2023 at 21:38

Destabilizers of the thymidylate synthase homodimer accelerate its proteasomal degradation and inhibit cancer growth.

Molecular and Cellular Modeling

Abstract (Expand)

Drugs that target human thymidylate synthase (hTS), a dimeric enzyme, are widely used in anticancer therapy. However, treatment with classical substrate-site-directed TS inhibitors induces over-expression …

Authors: L. Costantino, S. Ferrari, M. Santucci, O. M. H. Salo-Ahen, E. Carosati, S. Franchini, A. Lauriola, C. Pozzi, M. Trande, G. Gozzi, P. Saxena, G. Cannazza, L. Losi, D. Cardinale, A. Venturelli, A. Quotadamo, P. Linciano, L. Tagliazucchi, M. G. Moschella, R. Guerrini, S. Pacifico, R. Luciani, F. Genovese, S. Henrich, S. Alboni, N. Santarem, A. da Silva Cordeiro, E. Giovannetti, G. J. Peters, P. Pinton, A. Rimessi, G. Cruciani, R. M. Stroud, R. C. Wade, S. Mangani, G. Marverti, D. D'Arca, G. Ponterini, M. P. Costi

Date Published: 7th Dec 2022

Publication Type: Journal

PubMed ID: 36475542

Citation: Elife. 2022 Dec 7;11:e73862. doi: 10.7554/eLife.73862.

Created: 11th Jan 2023 at 08:32, Last updated: 27th Jan 2023 at 21:39

Identification of antiparasitic drug targets using a multi-omics workflow in the acanthocephalan model

Molecular and Cellular Modeling

Abstract (Expand)

Abstract Background With the expansion of animal production, parasitic helminths are gaining increasing economic importance. However, application of several established deworming agents can harm treated …er, application of several established deworming agents can harm treated hosts and environment due to their low specificity. Furthermore, the number of parasite strains showing resistance is growing, while hardly any new anthelminthics are being developed. Here, we present a bioinformatics workflow designed to reduce the time and cost in the development of new strategies against parasites. The workflow includes quantitative transcriptomics and proteomics, 3D structure modeling, binding site prediction, and virtual ligand screening. Its use is demonstrated for Acanthocephala (thorny-headed worms) which are an emerging pest in fish aquaculture. We included three acanthocephalans ( Pomphorhynchus laevis, Neoechinorhynchus agilis , Neoechinorhynchus buttnerae ) from four fish species (common barbel, European eel, thinlip mullet, tambaqui). Results The workflow led to eleven highly specific candidate targets in acanthocephalans. The candidate targets showed constant and elevated transcript abundances across definitive and accidental hosts, suggestive of constitutive expression and functional importance. Hence, the impairment of the corresponding proteins should enable specific and effective killing of acanthocephalans. Candidate targets were also highly abundant in the acanthocephalan body wall, through which these gutless parasites take up nutrients. Thus, the candidate targets are likely to be accessible to compounds that are orally administered to fish. Virtual ligand screening led to ten compounds, of which five appeared to be especially promising according to ADMET, GHS, and RO5 criteria: tadalafil, pranazepide, piketoprofen, heliomycin, and the nematicide derquantel. Conclusions The combination of genomics, transcriptomics, and proteomics led to a broadly applicable procedure for the cost- and time-saving identification of candidate target proteins in parasites. The ligands predicted to bind can now be further evaluated for their suitability in the control of acanthocephalans. The workflow has been deposited at the Galaxy workflow server under the URL tinyurl.com/yx72rda7 .

Authors: Hanno Schmidt, Katharina Mauer, Manuel Glaser, Bahram Sayyaf Dezfuli, Sören Lukas Hellmann, Ana Lúcia Silva Gomes, Falk Butter, Rebecca C. Wade, Thomas Hankeln, Holger Herlyn