Article
Chemistry, Multidisciplinary
Jeffrey O. Agushaka, Absalom E. Ezugwu
Summary: The initialisation control parameters play a significant role in improving the performance of population-based metaheuristic algorithms, yet there have been few studies in this area. This paper presents a comprehensive survey of different initialisation schemes, discusses their success levels and limitations, and provides useful insights for future research directions.
APPLIED SCIENCES-BASEL
(2022)
Article
Mathematics
Emanuel Vega, Ricardo Soto, Pablo Contreras, Broderick Crawford, Javier Pena, Carlos Castro
Summary: Population-based approaches offer new search strategies for optimization problems. This work proposes a hybrid architecture that intelligently balances population size by using learning components and statistical modeling methods. It demonstrates the viability and effectiveness of the approach through solving benchmark functions and the multidimensional knapsack problem.
Article
Chemistry, Multidisciplinary
Hongyan Du, Dejun Jiang, Odin Zhang, Zhenxing Wu, Junbo Gao, Xujun Zhang, Xiaorui Wang, Yafeng Deng, Yu Kang, Dan Li, Peichen Pan, Chang-Yu Hsieh, Tingjun Hou
Summary: Contemporary structure-based molecular generative methods have shown great potential in drug design. However, existing methods have limitations such as contradicting chemical intuition and relying on large-scale structural data. To overcome these challenges, researchers have proposed a novel search-based framework, 3D-MCTS, which employs a fragment-based molecular editing strategy and achieves remarkable results in generating molecules with enhanced binding affinity.
Article
Engineering, Multidisciplinary
Chao-Lung Yang, Atinkut Atinafu Yilma, Hendri Sutrisno, Bereket Haile Woldegiorgis, Thi Phuong Quyen Nguyen
Summary: Quick process shift detection is crucial in modern smart manufacturing. This research proposes LSTM-based models with metaheuristics optimizer for fast shift detection. The models were evaluated on various datasets and outperformed benchmark methods, confirming their effectiveness for real-world problems.
ALEXANDRIA ENGINEERING JOURNAL
(2023)
Article
Mathematics
Emanuel Vega, Ricardo Soto, Broderick Crawford, Javier Pena, Carlos Castro
Summary: The study introduces a novel optimisation framework called LB2, focusing on predicting better movements for improved performance. Testing with movement operators of a spotted hyena optimiser, the hybrid approach is found to be competitive compared to state-of-the-art algorithms and sequential parameter optimisation methods in solving benchmark functions.
Article
Biochemistry & Molecular Biology
Qizhi Zhang, Wenmei Yu, Zhenhua Liu, Hui Li, Yihui Liu, Xin Liu, Zhaoshun Han, Jun He, Yaofu Zeng, Yu Guo, Yunmei Liu
Summary: Photodynamic therapy is a promising treatment for tumors, and new porphyrin-chrysin photosensitizer derivatives have been synthesized in this study. Most of these compounds showed antitumor activity against HeLa and A549 cells, and compound 4c had the best photodynamic therapy effect. The binding of compounds to ct-DNA was correlated with their antitumor activity, and modifications to the porphyrin ring could enhance the activity.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Chemistry, Physical
Katarzyna Rzesikowska, Justyna Kalinowska-Tluscik, Anna Krawczuk
Summary: Computational methods, especially molecular docking-based calculations, are essential in modern drug discovery. The scoring function is a useful energy-based element in docking software for evaluating ligand-protein binding. However, the current scoring functions often lead to incorrect selection of hit molecules and poor pose prediction.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Multidisciplinary Sciences
Mohamed H. Baren, Seham A. Ibrahim, Munirah M. Al-Rooqi, Saleh A. Ahmed, Mohammed M. El-Gamil, Hend A. Hekal
Summary: In this study, a new series of α-aminophosphonates derivatives were synthesized and evaluated for their anticancer activities. Some compounds exhibited stronger inhibitory activity than Doxorubicin, and were found to potentially function as VEGFR2 and FGFR1 inhibitors.
SCIENTIFIC REPORTS
(2023)
Article
Chemistry, Physical
Shaghaf Mobin Ansari, Ghazala Khanum, Muneer-Ul-Shafi Bhat, Masood Ahmad Rizvi, Noor U. Din Reshi, Majid Ahmad Ganie, Saleem Javed, Bhahwal Ali Shah
Summary: In this study, the crystal structure of 1-(4-bromophenyl)-2a,8a-dihydrocyclobuta[b]naphthalene-3,8-dione was characterized using single crystal X-ray. Various spectroscopic techniques such as 13C and 1HNMR, UV-Vis, and IR were employed for characterization. Quantum chemical calculations were performed to predict the compound's structural, electronic, and vibrational properties. The significance of 1-(4-bromophenyl)-2a,8a-dihydrocyclobuta[b]naphthalene-3,8-dione in the management of Covid-19 disorders was also investigated. Molecular Dynamics Simulation was used to assess biomolecular stability. Rating: 7/10.
JOURNAL OF MOLECULAR STRUCTURE
(2023)
Article
Computer Science, Artificial Intelligence
Erik Cuevas, Hector Escobar, Ram Sarkar, Heba F. Eid
Summary: This paper proposes a new population initialization method for metaheuristic algorithms, where the initial set of candidate solutions is obtained through the sampling of the objective function. The method aims to find initial solutions that are close to the prominent values of the objective function, and these initial points represent promising regions of the search space. The proposed approach shows faster convergence and improved quality of solutions compared to other similar approaches.
APPLIED INTELLIGENCE
(2023)
Article
Computer Science, Information Systems
Xinxin Li, Shuai Hua, Qunfeng Liu, Yun Li
Summary: This paper proposes a partition-based convergence framework for population-based optimization algorithms to solve the issue of global convergence. The framework alternates between regular partitions and evolutions of populations, ensuring global convergence. The framework is applied to particle swarm optimization, differential evolution, and genetic algorithm, resulting in improved global convergence and performance compared to the original versions.
INFORMATION SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Fabian Audu Ugbe, Gideon Adamu Shallangwa, Adamu Uzairu, Ibrahim Abdulkadir, Emmanuel Israel Edache, Wafa Abdullah I. Al-Megrin, Samia T. Al-Shouli, Ying Wang, Mohnad Abdalla
Summary: This study evaluated the anti-leishmanial potential of organoselenium compounds using cheminformatic techniques. The results showed that the newly designed compounds exhibited good drug-likeness and pharmacokinetic profiles, and had good binding interactions with the target protein. These new compounds could be potential drug molecules for the treatment of leishmaniasis.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Multidisciplinary
Dejun Jiang, Zhaofeng Ye, Chang-Yu Hsieh, Ziyi Yang, Xujun Zhang, Yu Kang, Hongyan Du, Zhenxing Wu, Jike Wang, Yundian Zeng, Haotian Zhang, Xiaorui Wang, Mingyang Wang, Xiaojun Yao, Shengyu Zhang, Jian Wu, Tingjun Hou
Summary: This study compiled the largest metalloprotein-ligand complex dataset and evaluated the docking powers of three competitive docking tools for metalloproteins. A structure-based deep graph model called MetalProGNet was developed to predict metalloprotein-ligand interactions. MetalProGNet outperformed various baselines in internal and external evaluations. The study also employed an atom-atom interaction masking technique to interpret MetalProGNet.
Article
Biology
Sarah Hall-Swan, Didier Devaurs, Mauricio M. Rigo, Dinler A. Antunes, Lydia E. Kavraki, Geancarlo Zanatta
Summary: An unprecedented research effort has been made in response to the COVID-19 pandemic, focusing on crystallographic structures of SARS-CoV-2 proteins and virtual screening for potential drug inhibitors. Addressing receptor flexibility, a computational tool called DINC-COVID has been implemented for ensemble docking with success in identifying alternative binding modes. This work highlights the importance of considering receptor flexibility in docking studies and provides a platform for new inhibitors against SARS-CoV-2 proteins.
COMPUTERS IN BIOLOGY AND MEDICINE
(2021)
Article
Agricultural Engineering
Francisco Thalysson Tavares Cavalcante, Aluisio Marques da Fonseca, Jeferson Yves Nunes Holanda Alexandre, Jose C. S. dos Santos
Summary: Biolubricants derived from renewable raw materials and synthesized using enzymes have gained market attention. This study focuses on the synthesis reactions of biolubricants using the genetically-modified lipase Eversa (R) Transform 2.0. Computational tools, such as docking and molecular dynamics, were employed to understand the interactions and stability of enzyme-ligand complexes. In vitro validation confirmed the improved esterification activity of the lipase with isoamyl alcohol, suggesting its potential in the biolubricant production system.
INDUSTRIAL CROPS AND PRODUCTS
(2022)
Article
Multidisciplinary Sciences
Xiaojuan Hu, Maja-Olivia Lenz-Himmer, Carsten Baldauf
Summary: This study presents a dataset of amino-methylated and acetylated dipeptides of 20 proteinogenic amino acids, including their possible side chain protonation states and interactions with selected divalent cations. The data was generated through first-principles calculations and is suitable for force field parameterization and other applications. The metadata has been formalized in an ontology to make the data accessible across domains and machines.
Article
Chemistry, Medicinal
Hazem Ahmed, Livio Gisler, Nehal H. Elghazawy, Claudia Keller, Wolfgang Sippl, Steven H. Liang, Ahmed Haider, Simon M. Ametamey
Summary: GluN2B-enriched NMDARs are associated with several neurodegenerative and psychiatric diseases. In this study, a tritium-labeled form of OF-NB1 was developed as a selective GluN1/2B PET imaging agent. Competitive binding experiments and molecular simulations demonstrated the superior selectivity and performance of OF-NB1, making it a promising tool for screening potential GluN1/2B drug candidates.
Article
Multidisciplinary Sciences
Ekaterina Osipova, Rico Barsacchi, Tom Brown, Keren Sadanandan, Andrea H. Gaede, Amanda Monte, Julia Jarrells, Claudia Moebius, Martin Pippel, Douglas L. Altshuler, Sylke Winkler, Marc Bickle, Maude W. Baldwin, Michael Hiller
Summary: Hummingbirds have specific metabolic adaptations for their energy-demanding hovering flight, but the genomic changes responsible for these adaptations are not well understood. In this study, researchers generated a high-quality genome assembly of the long-tailed hermit hummingbird and identified a gene called FBP2 that was inactivated during the evolution of hovering flight. Knocking down FBP2 in avian muscle cells increased glycolysis and mitochondrial respiration, as well as the number of mitochondria. Additionally, genes related to mitochondrial respiration and organization were up-regulated in hummingbird flight muscle. These findings suggest that the loss of FBP2 was a key step in the evolution of the metabolic muscle adaptations necessary for true hovering flight.
Article
Chemistry, Organic
Mohamed Abdelsalam, Matthes Zessin, Matthias Schmidt, Mike Schutkowski, Wolfgang Sippl
Summary: The design and synthesis of a selective degrader of histone deacetylase-3 (HDAC3) using proteolysis targeting chimeras (PROTACs) is described in this study. The newly synthesized compound showed good inhibitory activity against HDAC3 but did not exhibit degradation for the targeted HDACs.
Editorial Material
Biochemistry & Molecular Biology
Wolfgang Sippl
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Nicole S. Paulat, Jessica M. Storer, Diana D. Moreno-Santillan, Austin B. Osmanski, Kevin A. M. Sullivan, Jenna R. Grimshaw, Jennifer Korstian, Michaela Halsey, Carlos J. Garcia, Claudia Crookshanks, Jaquelyn Roberts, Arian F. A. Smit, Robert Hubley, Jeb Rosen, Emma C. Teeling, Sonja C. Vernes, Eugene Myers, Martin Pippel, Thomas Brown, Michael Hiller, Danny Rojas, Liliana M. Davalos, Kerstin Lindblad-Toh, Elinor K. Karlsson, David A. Ray
Summary: Bats are a hotspot for horizontal transfer of DNA transposons, with over 200 putative HT elements found within bats. These events broadly coincide with the diversification of several bat clades, supporting the hypothesis that DNA transposon invasions have contributed to genetic diversification of bats.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Blair P. Bentley, Tomas Carrasco-Valenzuela, Elisa K. S. Ramos, Harvinder Pawar, Larissa Souza Arantes, Alana Alexander, Shreya M. Banerjee, Patrick Masterson, Martin Kuhlwilm, Martin Pippel, Jacquelyn Mountcastle, Bettina Haase, Marcela Uliano-Silva, Giulio Formenti, Kerstin Howe, William Chow, Alan Tracey, Ying Sims, Sarah Pelan, Jonathan Wood, Kelsey Yetsko, Justin R. Perrault, Kelly Stewart, Scott R. Benson, Yaniv Levy, Erica V. Todd, H. Bradley Shaffer, Peter Scott, Brian T. Henen, Robert W. Murphy, David W. Mohr, Alan F. Scott, David J. Duffy, Neil J. Gemmell, Alexander Suh, Sylke Winkler, Francoise Thibaud-Nissen, Mariana F. Nery, Tomas Marques-Bonet, Agostinho Antunes, Yaron Tikochinski, Peter H. Dutton, Olivier Fedrigo, Eugene W. Myers, Erich D. Jarvis, Camila J. Mazzoni, Lisa M. Komoroske
Summary: Sea turtles are ancient marine vertebrates that have evolved from terrestrial ancestors. Their unique physiological and ecological traits and the genomic basis behind them remain largely unknown. This study generated and analyzed high-quality reference genomes for leatherback and green turtles, revealing divergent evolution in certain gene families that may be responsible for immunological and sensory adaptations. Microchromosomes were found to play a critical role in vertebrate evolutionary adaptation. Furthermore, diversity and demographic histories differed significantly between the two species, indicating concerns over the persistence of leatherback turtles under future climate scenarios.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Chemistry, Medicinal
Mohamed Abdelsalam, Mariia Zmyslia, Karin Schmidtkunz, Anita Vecchio, Sebastian Hilscher, Hany S. Ibrahim, Mike Schutkowski, Manfred Jung, Claudia Jessen-Trefzer, Wolfgang Sippl
Summary: In this study, a series of prodrugs for class I histone deacetylases (HDACs) were designed and synthesized using known selective HDAC inhibitors. Compound 6 showed the most potent inhibitory activity against nitroreductase (NTR)-transfected leukemic cells.
ARCHIV DER PHARMAZIE
(2023)
Article
Biology
Demian Burguera, Francesco Dionigi, Kristina Kverkova, Sylke Winkler, Thomas Brown, Martin Pippel, Yicheng Zhang, Maxwell Shafer, Annika L. A. Nichols, Eugene Myers, Pavel Nemec, Zuzana Musilova
Summary: We found independent expansions producing large gene repertoires in several lineages of nocturnal amphibious fishes, generally able to perform active terrestrial exploration. Furthermore, we also detected an augmented information-processing capacity in the olfactory bulb of nocturnal amphibious fishes. Overall, we report a convergent genomic and phenotypic magnification of the olfactory system in nocturnal amphibious fishes.
Article
Plant Sciences
Jirina Zackova Suchanova, Gust Bilcke, Beata Romanowska, Ali Fatlawi, Martin Pippel, Alastair Skeffington, Michael Schroeder, Wim Vyverman, Klaas Vandepoele, Nils Kroeger, Nicole Poulsen
Summary: This study used various methods to investigate the evolutionary history and function of diatom adhesive proteins, and discovered a new protein family called Trailins, which contains a unique amino acid sequence acquired from bacteria. The findings provide new insights into the molecular basis for diatom biofilm formation.
Article
Genetics & Heredity
Anastasia T. Shatilovich, Vamshidhar V. Gade, Martin Pippel, Tarja Hoffmeyer, Alexei M. Tchesunov, Lewis Stevens, Sylke Winkler, Graham Hughes, Sofia H. Traikov, Michael W. Hiller, Elizaveta V. Rivkina, Philipp P. Schiffer, Eugene P. Myers, Teymuras P. Kurzchalia
Summary: Some organisms have developed the ability to survive in a suspended metabolism state called cryptobiosis in unfavorable environmental conditions. Nematodes from Siberian permafrost have been revived after being in cryptobiosis for thousands of years. Precise radiocarbon dating shows that these nematodes have remained in cryptobiosis since the late Pleistocene. Comparative analysis reveals that the molecular mechanisms for cryptobiosis in these nematodes are similar to that in C. elegans, and that C. elegans dauer larvae can remain viable for longer periods in suspended animation than previously reported.
Article
Oncology
Ramy Ashry, Al-Hassan M. Mustafa, Kristin Hausmann, Michael Linnebacher, Susanne Strand, Wolfgang Sippl, Matthias Wirth, Oliver H. Kraemer
Summary: Tumors in the pancreas and colon are still a clinical challenge. Different gene expression profiles between cancer cells and normal cells can be targeted by drugs that modulate protein acetylation. KH16 is a novel compound that induces hyperacetylation, leading to cell death in tumor cells while sparing normal cells. It shows superior efficacy compared to clinically established drugs. Further studies can focus on KH16 and similar compounds for cancer therapy.
Article
Chemistry, Medicinal
Emre F. F. Buelbuel, Dina Robaa, Ping Sun, Fereshteh Mahmoudi, Jelena Melesina, Matthes Zessin, Mike Schutkowski, Wolfgang Sippl
Summary: This study analyzed different ligand-based and structure-based drug design techniques to predict the binding mode and inhibitory activity of recently developed alkylhydrazide HDAC inhibitors. Alkylhydrazides have shown promising effects in various cancer cell lines. The created models, including pharmacophore models and atom-based quantitative structure-activity relationship (QSAR) models, explain in vitro data well and were used to develop novel HDAC3 inhibitors.
Article
Biology
Fady Baselious, Dina Robaa, Wolfgang Sippl
Summary: In this study, we optimized the HDAC11 AlphaFold model by adding the catalytic zinc ion and successfully generated stable complexes for docking of selective inhibitors. The most reasonable pose was selected based on structural comparison, and the model explained the binding behavior of known HDAC11 inhibitors.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Review
Chemistry, Multidisciplinary
Conrad V. Simoben, Smith B. Babiaka, Aurelien F. A. Moumbock, Cyril T. Namba-Nzanguim, Donatus Bekindaka Eni, Jose L. Medina-Franco, Stefan Guenther, Fidele Ntie-Kang, Wolfgang Sippl
Summary: The use of traditional medicine has a long history and is still relied upon by many, especially in developing or underprivileged communities. In silico-based methods have played a crucial role in drug discovery, particularly in identifying natural product-based candidates. However, there are challenges in identifying and proposing novel natural product-based hits.
