Article
Biochemistry & Molecular Biology
Nicolas Foloppe, I-Jen Chen
Summary: This study utilized molecular dynamics simulations to comprehensively investigate the reorganization energy of compounds upon binding to proteins, revealing negative reorganization enthalpies and demonstrating that intramolecular interactions may not necessarily oppose binding, but could stabilize the bound state. The results indicated a redistribution of interactions upon binding, with occasional larger reorganization values observed, suggesting a qualitative compatibility with binding.
BIOORGANIC & MEDICINAL CHEMISTRY
(2021)
Review
Biochemistry & Molecular Biology
Edward King, Erick Aitchison, Han Li, Ray Luo
Summary: The grand challenge of structure-based drug design lies in accurately predicting binding free energies. Molecular dynamics simulations have enabled the modeling of conformational changes in the binding process, leading to the calculation of thermodynamic quantities for estimating binding affinities. Various approaches, including MM-PBSA, LIE, and alchemical methods, have been widely used to model molecular recognition for drug discovery and lead optimization.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Ao Liu, Xin Meng, Chen-Chen Shen, Zhi-Yuan Zhang, Chunju Li
Summary: Heterogeneous macrocycles with fluorenone and fluorenol functional groups were synthesized using two facile methods. The resulting macrocycles exhibited intriguing intramolecular energy transfer and fluorescence enhancement, attributed to the well-matched absorption/emission spectra and close proximity of the fluorenone/fluorenol moieties.
CHEMICAL COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Huaichuan Duan, Kaixuan Hu, Dan Zheng, Yan Cheng, Zelan Zhang, Yueteng Wang, Li Liang, Jianping Hu, Ting Luo
Summary: In this study, the molecular recognition of hCNT3 with uridine was investigated using molecular docking and molecular dynamics simulations. Uridine derivatives with potentially high inhibitory activity were designed. The study revealed the molecular interactions between uridine and hCNT3 and provided potential lead compounds for anti-cancer drug development.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Virology
Qinfang Sun, Ronald M. Levy, Karen A. Kirby, Zhengqiang Wang, Stefan G. Sarafianos, Nanjie Deng
Summary: This study demonstrates that drug resistance to the HIV-1 capsid-targeting antiviral GS-6207 is mainly caused by the free energy cost of drug-induced protein side chain reorganization in the mutant protein. The resistance mutation M66I leads to a significant suppression of GS-6207 antiviral activity, highlighting the importance of side chain reorganization in drug resistance mechanisms.
Article
Chemistry, Physical
Javier Alvarez-Conde, Andres Garzon-Ruiz, Amparo Navarro, Sonia B. Jimenez-Pulido, Pablo Gonzalez-Rodriguez, Juan Cabanillas-Gonzalez, Eva M. Garcia-Frutos
Summary: This work presents the synthesis, characterization, and theoretical calculations of two new diyne bridged azaindole derivatives. The study reveals that the presence of a diyne group leads to low rotational barrier and large conformational variability. The vibrational stretching mode of the diyne bridge has a significant contribution to non-radiative relaxation and weak fluorescence observed from the compounds.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Biochemistry & Molecular Biology
Niyi Adelakun, Ikponwmosa Obaseki, Ayobami Adeniyi, Oluwaseun Fapohunda, Eseiwi Obaseki, Olaposi Omotuyi
Summary: This study employed structural bioinformatics methods to identify potential allosteric USP14 inhibitors and investigated their stability and interactions with USP14 through molecular dynamics simulation. The results showed that two lead compounds exhibited improved binding affinity and maintained stability during the simulation. In-silico pharmacological evaluation further indicated that these compounds have promising pharmacological properties.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Chemistry, Organic
Francisco A. Martins, Lucas de Azevedo Santos, Daniela Rodrigues Silva, Celia Fonseca Guerra, F. Matthias Bickelhaupt, Matheus P. Freitas
Summary: The gauche conformer in 1-X,2-Y-disubstituted ethanes is only favored for relatively small substituents, while the anti conformer is generally favored for larger substituents. In 2-iodoethanol, the gauche conformer is preferred when the hydroxyl hydrogen is oriented toward the iodine atom.
JOURNAL OF ORGANIC CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Ankita Agarwal, Suresh Alagar, Shri Kant, Ranjit Prasad Bahadur
Summary: This study investigates the molecular mechanism of interaction between the N-terminal tandem RNA-recognition motifs (tRRMs) of HuR and mRNA using molecular dynamics simulation. The researchers also explore the effect of point mutations on the binding specificity of HuR-mRNA interactions. The findings reveal that certain mutations significantly affect the binding affinity due to unfavorable conformations and loss of critical interactions.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Rohit Shukla, Harish Shukla, Timir Tripathi
Summary: Mycobacterium tuberculosis remains a successful bacterial pathogen with drug-resistant strains being a major issue; however, phenyl-diketo acid (PDKA) analogs show promise as anti-TB compounds, potentially serving as lead compounds for drug discovery against TB.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Review
Pharmacology & Pharmacy
Zhiwei Yang, Zichen Zhang, Yizhen Zhao, Qiushi Ye, Xuhua Li, Lingjie Meng, Jiangang Long, Shengli Zhang, Lei Zhang
Summary: Interactions between organelles are crucial for maintaining normal cell function and homeostasis, and they are also implicated in various diseases and drug discovery. Advanced imaging techniques and fluorescent probes have enabled accurate estimation of subcellular structures, organelle interactions, and drug discovery related to organelles. This study summarizes recent advances in this rapidly evolving field, highlighting the potential of nanoscopy and molecular dynamics simulations in organelle-related drug discovery.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Selvaraj Alagu Lakshmi, Raja Mohamed Beema Shafreen, Arumugam Priya, Karutha Pandian Shunmugiah
Summary: The study explored the interaction of active components from Indian medicinal plants for treating respiratory disorders, identifying potential compounds like Cucurbitacin E and orientin that show promise in inhibiting SARS-CoV-2.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Biochemistry & Molecular Biology
Kiran Bharat Lokhande, Ashish Shrivastava, Ashutosh Singh
Summary: Monkeypox virus (MPXV) outbreak outside endemic areas poses a global public health emergency. Lack of effective treatment for this zoonotic infection necessitates urgent discovery of new medications. This study uses advanced computational techniques to identify potential lead compounds targeting key MPXV proteins. The findings provide valuable insights for drug development and treatment of human MPXV infection.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Dipanjan Mukherjee, Priya Singh, Soumendra Singh, Debanjona Singh Roy, Subhankar Singha, Uttam Pal, Jhimli Sengupta, Rami J. Obaid, Saleh A. Ahmed, Tanusri Saha Dasgupta, Ranjan Das, Samir Kumar Pal
Summary: The study investigates the molecular recognition and binding process between CD1 and HSA, revealing that different host vehicles can impact the rate of drug binding to the protein, thereby modulating the release rate of the drug mimic.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Review
Biochemistry & Molecular Biology
Ge Wang, Yuhao Bai, Jiarui Cui, Zirui Zong, Yuan Gao, Zhen Zheng
Summary: This review provides an overview of the importance of the RAS gene family and its relevance to cancer development, as well as the challenges in designing drugs targeting RAS. Computer-aided drug design (CADD) offers new approaches for finding RAS-targeted drugs.