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Journal of Biomolecular Structure and Dynamics Volume 36, 2018 - Issue 10
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Letter to the Editor

MM-GBSA and MM-PBSA performance in activity evaluation of AMPA receptor positive allosteric modulators

Dmitry S. KarlovDepartment of Chemistry, Lomonosov Moscow State University, 1 Build. 3, Leninskie Gory, Moscow, 119991Russian Federation;Institute of Physiologically Active Compounds, Russian Academy of Sciences, 1 Severny proezd, Chernogolovka, Moscow Region142432, Russian FederationORCID Iconhttp://orcid.org/0000-0002-7194-1081
ORCID Icon,
Mstislav I. LavrovDepartment of Chemistry, Lomonosov Moscow State University, 1 Build. 3, Leninskie Gory, Moscow, 119991Russian Federation;Institute of Physiologically Active Compounds, Russian Academy of Sciences, 1 Severny proezd, Chernogolovka, Moscow Region142432, Russian Federation
,
Vladimir A. PalyulinDepartment of Chemistry, Lomonosov Moscow State University, 1 Build. 3, Leninskie Gory, Moscow, 119991Russian Federation;Institute of Physiologically Active Compounds, Russian Academy of Sciences, 1 Severny proezd, Chernogolovka, Moscow Region142432, Russian FederationCorrespondence[email protected]
ORCID Iconhttp://orcid.org/0000-0001-8792-8386
ORCID Icon &
Nikolay S. ZefirovDepartment of Chemistry, Lomonosov Moscow State University, 1 Build. 3, Leninskie Gory, Moscow, 119991Russian Federation;Institute of Physiologically Active Compounds, Russian Academy of Sciences, 1 Severny proezd, Chernogolovka, Moscow Region142432, Russian Federation
Pages 2508-2516 | Received 06 Mar 2017, Accepted 21 Jul 2017, Published online: 10 Aug 2017

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Mahendra Kumar Meena, Durgesh Kumar, Abhilash Jayaraj, Ajay Kumar, Kamlesh Kumari, L. M. Katata-Seru, Indra Bahadur, Vinod Kumar, Anjali Sherawat & Prashant Singh. (2022) Designed thiazolidines: an arsenal for the inhibition of nsP3 of CHIKV using molecular docking and MD simulations. Journal of Biomolecular Structure and Dynamics 40:4, pages 1607-1616.
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Revanth Bathula, Goverdhan Lanka, Narasimha Muddagoni, Mahendar Dasari, Sravanthi Nakkala, Manan Bhargavi, Gururaj Somadi, Sree Kanth Sivan & Sarita Rajender Potlapally. (2020) Identification of potential Aurora kinase-C protein inhibitors: an amalgamation of energy minimization, virtual screening, prime MMGBSA and AutoDock. Journal of Biomolecular Structure and Dynamics 38:8, pages 2314-2325.
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D.S. Karlov, O.I. Barygin, M.Y. Dron, V.A. Palyulin, V.V. Grigoriev & M.V. Fedorov. (2019) Short peptide with an inhibitory activity on the NMDA/Gly-induced currents. SAR and QSAR in Environmental Research 30:9, pages 683-695.
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Pavithra K. Balasubramanian, Anand Balupuri, Swapnil P. Bhujbal & Seung Joo Cho. (2019) 3D-QSAR-aided design of potent c-Met inhibitors using molecular dynamics simulation and binding free energy calculation. Journal of Biomolecular Structure and Dynamics 37:8, pages 2165-2178.
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Tian-Tian Zhao, Hao-Jie Hu, Li-Xin Gao, Yu-Bo Zhou, Yun-Long Zhu, Chun Zhang, Jia Li & Wen-Long Wang. (2023) Exploring the mechanism of the PTP1B inhibitors by molecular dynamics and experimental study. Journal of Molecular Graphics and Modelling 125, pages 108585.
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Elena A. Golubeva, Mstislav I. Lavrov, Eugene V. Radchenko & Vladimir A. Palyulin. (2022) Diversity of AMPA Receptor Ligands: Chemotypes, Binding Modes, Mechanisms of Action, and Therapeutic Effects. Biomolecules 13:1, pages 56.
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Kseniya N. Sedenkova, Denis V. Zverev, Anna A. Nazarova, Mstislav I. Lavrov, Eugene V. Radchenko, Yuri K. Grishin, Alexey V. Gabrel’yan, Vladimir L. Zamoyski, Vladimir V. Grigoriev, Elena B. Averina & Vladimir A. Palyulin. (2022) Novel Nanomolar Allosteric Modulators of AMPA Receptor of Bis(pyrimidine) Series: Synthesis, Biotesting and SAR Analysis. Molecules 27:23, pages 8252.
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Dmitry S. Karlov, Nadezhda S. Temnyakova, Dmitry A. Vasilenko, Oleg I. Barygin, Mikhail Y. Dron, Arseniy S. Zhigulin, Elena B. Averina, Yuri K. Grishin, Vladimir V. Grigoriev, Alexey V. Gabrel'yan, Viktor A. Aniol, Natalia V. Gulyaeva, Sergey V. Osipenko, Yury I. Kostyukevich, Vladimir A. Palyulin, Petr A. Popov & Maxim V. Fedorov. (2022) Biphenyl scaffold for the design of NMDA-receptor negative modulators: molecular modeling, synthesis, and biological activity. RSC Medicinal Chemistry 13:7, pages 822-830.
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Mstislav I. Lavrov, Polina N. Veremeeva, Elena A. Golubeva, Eugene V. Radchenko, Vladimir L. Zamoyski, Vladimir V. Grigoriev & Vladimir A. Palyulin. (2022) Positive and negative AMPA receptor modulators based on tricyclic bispidine derivative: Minor structural change inverts the type of activity. Mendeleev Communications 32:3, pages 360-363.
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Dmitry A. Vasilenko, Kirill S. Sadovnikov, Kseniya N. Sedenkova, Dmitry S. Karlov, Eugene V. Radchenko, Yuri K. Grishin, Victor B. Rybakov, Tamara S. Kuznetsova, Vladimir L. Zamoyski, Vladimir V. Grigoriev, Vladimir A. Palyulin & Elena B. Averina. (2021) A Facile Approach to Bis(isoxazoles), Promising Ligands of the AMPA Receptor. Molecules 26:21, pages 6411.
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E.V. Radchenko, A.S. Tarakanova, D.S. Karlov, M.I. Lavrov & V.A. Palyulin. (2021) Ligands of the AMPA-subtype glutamate receptors: mechanisms of action and novel chemotypes. Biomeditsinskaya Khimiya 67:3, pages 187-200.
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Mingyu Wu, Yu Sun, Meiru Zhu, Laiyu Zhu, Junhong Lü & Feng Geng. (2021) Molecular Dynamics-Based Allosteric Prediction Method to Design Key Residues in Threonine Dehydrogenase for Amino-Acid Production. ACS Omega 6:16, pages 10975-10983.
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Nadezhda S. Temnyakova, Dmitry A. Vasilenko, Mstislav I. Lavrov, Dmitry S. Karlov, Yuri K. Grishin, Vladimir L. Zamoyski, Vladimir V. Grigoriev, Elena B. Averina & Vladimir A. Palyulin. (2021) Novel bivalent positive allosteric AMPA receptor modulator of bis-amide series. Mendeleev Communications 31:2, pages 216-218.
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Vladimir Burmistrov, Christophe Morisseau, Dmitry Karlov, Dmitry Pitushkin, Andrey Vernigora, Elena Rasskazova, Gennady M. Butov & Bruce D. Hammock. (2020) Bioisosteric substitution of adamantane with bicyclic lipophilic groups improves water solubility of human soluble epoxide hydrolase inhibitors. Bioorganic & Medicinal Chemistry Letters 30:18, pages 127430.
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Vladimir P. Berishvili, Alexander N. Kuimov, Andrew E. Voronkov, Eugene V. Radchenko, Pradeep Kumar, Yahya E. Choonara, Viness Pillay, Ahmed Kamal & Vladimir A. Palyulin. (2020) Discovery of Novel Tankyrase Inhibitors through Molecular Docking-Based Virtual Screening and Molecular Dynamics Simulation Studies. Molecules 25:14, pages 3171.
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Yuzhou Huang, Hanxun Wang, Huibin Wang, Rui Wen, Xiaohui Geng, Tianci Huang, Jiyue Shi, Xiujun Wang & Jian Wang. (2020) Structure-based virtual screening of natural products as potential stearoyl-coenzyme a desaturase 1 (SCD1) inhibitors. Computational Biology and Chemistry 86, pages 107263.
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Dmitry S. Karlov, Sergey Sosnin, Maxim V. FedorovPetr Popov. (2020) graphDelta: MPNN Scoring Function for the Affinity Prediction of Protein–Ligand Complexes. ACS Omega 5:10, pages 5150-5159.
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Mstislav I. Lavrov, Dmitry S. Karlov, Tatiana A. Voronina, Vladimir V. Grigoriev, Aleksey A. Ustyugov, Sergey O. Bachurin & Vladimir A. Palyulin. (2019) Novel Positive Allosteric Modulators of AMPA Receptors Based on 3,7-Diazabicyclo[3.3.1]nonane Scaffold. Molecular Neurobiology 57:1, pages 191-199.
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Mstislav I. Lavrov, Polina N. Veremeeva, Dmitry S. Karlov, Vladimir L. Zamoyski, Vladimir V. Grigoriev & Vladimir A. Palyulin. (2019) Tricyclic derivatives of bispidine as AMPA receptor allosteric modulators. Mendeleev Communications 29:6, pages 619-621.
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Abdul-Akim D. Guseynov, Sergey A. Pisarev, Dmitry A. Shulga, Vladimir A. Palyulin, Maxim V. Fedorov & Dmitry S. Karlov. (2019) Computational characterization of the glutamate receptor antagonist perampanel and its close analogs: density functional exploration of conformational space and molecular docking study. Journal of Molecular Modeling 25:10.
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Pavithra K. Balasubramanian, Yeongjoon Lee & Yangmee Kim. (2019) Identification of Ligand‐binding Hotspot Residues of CDK4 Using Molecular Docking and Molecular Dynamics Simulation. Bulletin of the Korean Chemical Society 40:10, pages 1025-1032.
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Anna A. Nazarova, Kseniya N. Sedenkova, Dmitry S. Karlov, Mstislav I. Lavrov, Yuri K. Grishin, Tamara S. Kuznetsova, Vladimir L. Zamoyski, Vladimir V. Grigoriev, Elena B. Averina & Vladimir A. Palyulin. (2019) Bivalent AMPA receptor positive allosteric modulators of the bis(pyrimidine) series. MedChemComm 10:9, pages 1615-1619.
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Vladimir P. Berishvili, Valentin O. Perkin, Andrew E. Voronkov, Eugene V. Radchenko, Riyaz Syed, Chittireddy Venkata Ramana Reddy, Viness Pillay, Pradeep Kumar, Yahya E. Choonara, Ahmed Kamal & Vladimir A. Palyulin. (2019) Time-Domain Analysis of Molecular Dynamics Trajectories Using Deep Neural Networks: Application to Activity Ranking of Tankyrase Inhibitors. Journal of Chemical Information and Modeling 59:8, pages 3519-3532.
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