The future of molecular dynamics simulations in drug discovery.

J Comput Aided Mol Des

D. E. Shaw Research, New York, NY 10036, USA.

Published: January 2012

Molecular dynamics simulations can now track rapid processes--those occurring in less than about a millisecond--at atomic resolution for many biologically relevant systems. These simulations appear poised to exert a significant impact on how new drugs are found, perhaps even transforming the very process of drug discovery. We predict here future results we can expect from, and enhancements we need to make in, molecular dynamics simulations over the coming 25 years, and in so doing set out several Grand Challenges for the field. In the context of the problems now facing the pharmaceutical industry, we ask how we can best address drug discovery needs of the next quarter century using molecular dynamics simulations, and we suggest some possible approaches.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3268975PMC
http://dx.doi.org/10.1007/s10822-011-9517-yDOI Listing

Publication Analysis

Top Keywords

molecular dynamics
16
dynamics simulations
16
drug discovery
12
simulations
5
future molecular
4
dynamics
4
simulations drug
4
discovery molecular
4
simulations track
4
track rapid
4

Similar Publications

Chronic lymphocytic leukemia (CLL) is a malignancy caused by the overexpression of the anti-apoptotic protein B-cell lymphoma-2 (BCL-2), making it a critical therapeutic target. This study integrates computational screening, molecular docking, and molecular dynamics to identify and validate novel BCL-2 inhibitors from the ChEMBL database. Starting with 836 BCL-2 inhibitors, we performed ADME and Lipinski's Rule of Five (RO5) filtering, clustering, maximum common substructure (MCS) analysis, and machine learning models (Random Forest, SVM, and ANN), yielding a refined set of 124 compounds.

View Article and Find Full Text PDF

SH2 (Src Homology 2) domains play a crucial role in phosphotyrosine-mediated signaling and have emerged as promising drug targets, particularly in cancer therapy. STAT3 (Signal Transducer and Activator of Transcription 3), which contains an SH2 domain, plays a pivotal role in cancer progression and immune evasion because it facilitates the dimerization of STAT3, which is essential for their activation and subsequent nuclear translocation. SH2 domain-mediated STAT3 inhibition disrupts this binding, reduces phosphorylation of STAT3, and impairs dimerization.

View Article and Find Full Text PDF

Targeted Enrichment Sequencing Utilizing a Respiratory Pathogen Panel for Genomic Wastewater-Based Viral Epidemiology in Uruguay.

Food Environ Virol

January 2025

Laboratorio de Ecología Viral y Virus Zoonóticos, Unidad Académica de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Av. Alfredo Navarro 3051, 11600, Montevideo, Uruguay.

Human respiratory and enteric viruses are responsible for substantial morbidity and mortality worldwide. Wastewater-based epidemiology utilizing next-generation sequencing serves as an effective tool for monitoring viral circulation dynamics at the community level. However, these complex environmental samples are often laden with other microorganisms and host genomic material, which can hinder the sensitivity of viral detection.

View Article and Find Full Text PDF

Molecular Dynamics (MD) simulations are now widely utilized in pharmaceutical nanotechnology to gain deeper understanding of nanoscale processes imperative to drug design. This review has also detailed how MD simulation can be employed in the study of drug-nanocarrier interactions, controlling release of chemical compounds from drug delivery systems and increasing solubility and bioavailability of nanocarriers. Furthermore, MD contributes to examining the drug delivery systems, measuring the toxic effects, and determining biocompatibility of nanomedical systems.

View Article and Find Full Text PDF

Response of Amblyseius swirskii to deltamethrin.

Pest Manag Sci

January 2025

Unidad Mixta Gestión Biotecnológica de Plagas UV-IVIA, Department of Genetics, Institut de Biotecnologia i Biomedicina, Universitat de València, Valencia, Spain.

Background: The rising demand for environmentally friendly pest control highlights the importance of understanding the interaction between natural enemies and pesticides. Amblyseius swirskii, a predatory mite extensively used in biocontrol, plays a crucial role in managing pest populations in agricultural systems. Integrating this mite with selective pesticide use within integrated pest management (IPM) would significantly advance pest control and may reduce pesticide residues in the environment and agricultural produce.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!