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Prasanna A, Karunakar P, Pillai A, Mukundan S, Y V M, Balaji R, Niranjan V, Skariyachan S, Narayanappa R. Screening of bioactive compounds from selected mushroom species against putative drug targets in Mycobacterium tuberculosis: a multi-target approach. J Biomol Struct Dyn 2024:1-16. [PMID: 38895953 DOI: 10.1080/07391102.2024.2335292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 03/20/2024] [Indexed: 06/21/2024]
Abstract
Mycobacterium tuberculosis (Mtb) is a notorious pathogen that causes one of the highest mortalities globally. Due to a pressing demand to identify novel therapeutic alternatives, the present study aims to focus on screening the putative drug targets and prioritizing their role in antibacterial drug development. The most vital proteins involved in the Biotin biosynthesis pathway and the Lipoarabinomannan (LAM) pathway such as biotin synthase (bioB) and alpha-(1->6)-mannopyranosyltransferase A (mptA) respectively, along with other essential virulence proteins of Mtb were selected as drug targets. Among these, the ones without native structures were modelled and validated using standard bioinformatics tools. Further, the interactions were performed with naturally available lead molecules present in selected mushroom species such as Agaricus bisporus, Pleurotus djamor, Hypsizygus ulmarius. Through Gas Chromatography-Mass Spectrometry (GC-MS), 15 bioactive compounds from the methanolic extract of mushrooms were identified. Further, 4 were selected based on drug-likeness and pharmacokinetic screening for molecular docking analysis against our prioritized targets wherein Benz[e]azulene from Pleurotus djamor illustrated a good binding affinity with a LF rank score of -9.036 kcal mol -1 against nuoM (NADH quinone oxidoreductase subunit M) and could be used as a prospective candidate in order to combat Tuberculosis (TB). Furthermore, the stability of the complex are validated using MD Simulations and subsequently, the binding free energy was calculated using MM-GBSA analysis. Thus, the current in silico analysis suggests a promising role of compounds extracted from mushrooms in tackling the TB burden.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Akshatha Prasanna
- Department of Biotechnology, Dayananda Sagar College of Engineering (Affiliated to Visvesvaraya Technological University, Belagavi), Bengaluru, Karnataka, India
| | - Prashantha Karunakar
- Department of Biotechnology, Dayananda Sagar College of Engineering (Affiliated to Visvesvaraya Technological University, Belagavi), Bengaluru, Karnataka, India
| | - Anushka Pillai
- Department of Biotechnology, Dayananda Sagar College of Engineering (Affiliated to Visvesvaraya Technological University, Belagavi), Bengaluru, Karnataka, India
| | - Shreyashree Mukundan
- Department of Biotechnology, Dayananda Sagar College of Engineering (Affiliated to Visvesvaraya Technological University, Belagavi), Bengaluru, Karnataka, India
| | - Mansi Y V
- Department of Biotechnology, Dayananda Sagar College of Engineering (Affiliated to Visvesvaraya Technological University, Belagavi), Bengaluru, Karnataka, India
| | - Renu Balaji
- Department of Biotechnology, Dayananda Sagar College of Engineering (Affiliated to Visvesvaraya Technological University, Belagavi), Bengaluru, Karnataka, India
| | - Vidya Niranjan
- Department of Biotechnology, RV College of Engineering, Bengaluru, Karnataka, India
| | - Sinosh Skariyachan
- Department of Microbiology, St. Pius X College Rajapuram, Kasaragod, Kerala, India
| | - Rajeswari Narayanappa
- Department of Biotechnology, Dayananda Sagar College of Engineering (Affiliated to Visvesvaraya Technological University, Belagavi), Bengaluru, Karnataka, India
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2
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Zampieri D, Romano M, Fortuna S, Amata E, Dichiara M, Cosentino G, Marrazzo A, Mamolo MG. Design, Synthesis, and Cytotoxic Assessment of New Haloperidol Analogues as Potential Anticancer Compounds Targeting Sigma Receptors. Molecules 2024; 29:2697. [PMID: 38893570 PMCID: PMC11173765 DOI: 10.3390/molecules29112697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024] Open
Abstract
Sigma receptors (SRs), including SR1 and SR2 subtypes, have attracted increasing interest in recent years due to their involvement in a wide range of activities, including the modulation of opioid analgesia, neuroprotection, and potential anticancer activity. In this context, haloperidol (HAL), a commonly used antipsychotic drug, also possesses SR activity and cytotoxic effects. Herein, we describe the identification of novel SR ligands, obtained by a chemical hybridization approach. There wereendowed with pan-affinity for both SR subtypes and evaluated their potential anticancer activity against SH-SY5Y and HUH-7 cancer cell lines. Through a chemical hybridization approach, we identified novel compounds (4d, 4e, 4g, and 4j) with dual affinity for SR1 and SR2 receptors. These compounds were subjected to cytotoxicity testing using a resazurin assay. The results revealed potent cytotoxic effects against both cancer cell lines, with IC50 values comparable to HAL. Interestingly, the cytotoxic potency of the novel compounds resembled that of the SR1 antagonist HAL rather than the SR2 agonist siramesine (SRM), indicating the potential role of SR1 antagonism in their mechanism of action. The further exploration of their structure-activity relationships and their evaluation in additional cancer cell lines will elucidate their therapeutic potential and may pave the way for the development of novel anticancer agents that target SRs.
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Affiliation(s)
- Daniele Zampieri
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy;
| | - Maurizio Romano
- Department of Life Sciences, University of Trieste, Via Valerio 28, 34127 Trieste, Italy;
| | - Sara Fortuna
- Cresset-New Cambridge House, Bassingbourn Road, Litlington, Cambridge SG8 0SS, UK;
| | - Emanuele Amata
- Department of Drug and Health Sciences, University of Catania, Viale Doria 6, 95125 Catania, Italy; (E.A.); (M.D.); (G.C.); (A.M.)
| | - Maria Dichiara
- Department of Drug and Health Sciences, University of Catania, Viale Doria 6, 95125 Catania, Italy; (E.A.); (M.D.); (G.C.); (A.M.)
| | - Giuseppe Cosentino
- Department of Drug and Health Sciences, University of Catania, Viale Doria 6, 95125 Catania, Italy; (E.A.); (M.D.); (G.C.); (A.M.)
| | - Agostino Marrazzo
- Department of Drug and Health Sciences, University of Catania, Viale Doria 6, 95125 Catania, Italy; (E.A.); (M.D.); (G.C.); (A.M.)
| | - Maria Grazia Mamolo
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy;
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Woods CJ, Hedges LO, Mulholland AJ, Malaisree M, Tosco P, Loeffler HH, Suruzhon M, Burman M, Bariami S, Bosisio S, Calabro G, Clark F, Mey ASJS, Michel J. Sire: An interoperability engine for prototyping algorithms and exchanging information between molecular simulation programs. J Chem Phys 2024; 160:202503. [PMID: 38814008 DOI: 10.1063/5.0200458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 04/29/2024] [Indexed: 05/31/2024] Open
Abstract
Sire is a Python/C++ library that is used both to prototype new algorithms and as an interoperability engine for exchanging information between molecular simulation programs. It provides a collection of file parsers and information converters that together make it easier to combine and leverage the functionality of many other programs and libraries. This empowers researchers to use sire to write a single script that can, for example, load a molecule from a PDBx/mmCIF file via Gemmi, perform SMARTS searches via RDKit, parameterize molecules using BioSimSpace, run GPU-accelerated molecular dynamics via OpenMM, and then display the resulting dynamics trajectory in a NGLView Jupyter notebook 3D molecular viewer. This functionality is built on by BioSimSpace, which uses sire's molecular information engine to interconvert with programs such as GROMACS, NAMD, Amber, and AmberTools for automated molecular parameterization and the running of molecular dynamics, metadynamics, and alchemical free energy workflows. Sire comes complete with a powerful molecular information search engine, plus trajectory loading and editing, analysis, and energy evaluation engines. This, when combined with an in-built computer algebra system, gives substantial flexibility to researchers to load, search for, edit, and combine molecular information from multiple sources and use that to drive novel algorithms by combining functionality from other programs. Sire is open source (GPL3) and is available via conda and at a free Jupyter notebook server at https://try.openbiosim.org. Sire is supported by the not-for-profit OpenBioSim community interest company.
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Affiliation(s)
- Christopher J Woods
- Advanced Computing Research Centre, University of Bristol, Bristol, United Kingdom
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, United Kingdom
- OpenBioSim Community Interest Company, Edinburgh, United Kingdom
| | - Lester O Hedges
- Advanced Computing Research Centre, University of Bristol, Bristol, United Kingdom
- OpenBioSim Community Interest Company, Edinburgh, United Kingdom
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, United Kingdom
| | - Maturos Malaisree
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, United Kingdom
| | | | | | | | - Matthew Burman
- OpenBioSim Community Interest Company, Edinburgh, United Kingdom
| | - Sofia Bariami
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, United Kingdom
| | - Stefano Bosisio
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, United Kingdom
| | - Gaetano Calabro
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, United Kingdom
| | - Finlay Clark
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, United Kingdom
| | - Antonia S J S Mey
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, United Kingdom
| | - Julien Michel
- OpenBioSim Community Interest Company, Edinburgh, United Kingdom
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, United Kingdom
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Falsaperla R, Sortino V, Marino SD, Collotta AD, Gammeri C, Sipala FM, Volti GL, Ruggieri M, Ronsisvalle S. Molecular Dynamic Simulations to Determine Individualized Therapy: Tetrabenazine for the GNAO1 Encephalopathy E246K Variant. Mol Diagn Ther 2024; 28:329-337. [PMID: 38581611 DOI: 10.1007/s40291-024-00706-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2024] [Indexed: 04/08/2024]
Abstract
INTRODUCTION GNAO1 encephalopathy is characterized by severe hypotonia, psychomotor retardation, epilepsy, and movement disorders. Genetic variations in GNAO1 have been linked to neurological symptoms including movement disorders like dystonia. The correlation between the E246K mutation in the Gα subunit and aberrant signal transduction of G proteins has been established but no data are reported regarding the efficacy of medical treatment with tetrabenazine. METHODS Molecular modeling studies were performed to elucidate the molecular mechanisms underlying this mutation. We developed drug efficacy models using molecular dynamic simulations that replicated the behavior of wild-type and mutated proteins in the presence or absence of ligands. RESULTS AND DISCUSSION We demonstrated that the absence of the mutation leads to normal signal transduction upon receptor activation by the endogenous ligand, but not in the presence of tetrabenazine. In contrast, the presence of the mutation resulted in abnormal signal transduction in the presence of the endogenous ligand, which was corrected by the drug tetrabenazine. Tetrabenazine was identified as a promising therapeutic option for pediatric patients suffering from encephalopathy due to an E246K mutation in the GNAO1 gene validated through molecular dynamics. This is a potential first example of the use of this technique in a rare neurological pediatric disease.
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Affiliation(s)
- Raffaele Falsaperla
- Neonatal Intensive Care Unit and Neonatal Accompaniment Unit, Azienda Ospedaliero-Universitaria Policlinico "Rodolico-San Marco", San Marco Hospital, University of Catania, Catania, Italy.
- Unit of Clinical Paediatrics, Azienda Ospedaliero-Universitaria Policlinico, "Rodolico-San Marco", San Marco Hospital, Catania, Italy.
- Pediatric Clinic, University of Ferrara, Ferrara, Italy.
| | - Vincenzo Sortino
- Unit of Clinical Paediatrics, Azienda Ospedaliero-Universitaria Policlinico, "Rodolico-San Marco", San Marco Hospital, Catania, Italy
| | - Simona Domenica Marino
- Unit of Clinical Paediatrics, Azienda Ospedaliero-Universitaria Policlinico, "Rodolico-San Marco", San Marco Hospital, Catania, Italy
| | - Ausilia Desiree Collotta
- Unit of Clinical Paediatrics, Azienda Ospedaliero-Universitaria Policlinico, "Rodolico-San Marco", San Marco Hospital, Catania, Italy
- Postgraduate Training Program in Pediatrics, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Carmela Gammeri
- Postgraduate Training Program in Pediatrics, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Federica Maria Sipala
- Department of Drug and Health Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
| | - Giovanni Li Volti
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 87, 95125, Catania, Italy
| | - Martino Ruggieri
- Unit of Clinical Pediatrics, Unit of Rare Diseases, AOU "Policlinico", PO "G. Rodolico", University of Catania, Catania, Italy
| | - Simone Ronsisvalle
- Department of Drug and Health Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
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5
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Shaimardanov AR, Shulga DA, Palyulin VA. Do electrostatic interactions make a difference in physics-based AutoDock4 scoring function? J Comput Chem 2024. [PMID: 38661234 DOI: 10.1002/jcc.27373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024]
Abstract
Physics-based scoring function AutoDock4 is one of the most successfully applied tools in the area of structure-based drug design. However, current scoring functions are still far from being perfect. In a recent work highlighting the strengths and deficiencies of current scoring functions, we discovered that the residual error of ΔGbind predictions made by AutoDock4 is highly correlated to the presence of formally charged fragments in a ligand. In this work, we study how the use of the high-quality atomic charges, applied for contemporary force fields calculation, affects the quality of the experimental ΔGbind prediction by means of AutoDock4. We initially expected that the previously found discrepancy could be attributed to the Gasteiger charges used within AutoDock4. We show that AutoDock4 is, surprisingly, not sensitive to the charges used, and the use of QC-derived atomic charges does not lead to any statistical improvements. We also briefly discuss the role of the explicit empirical hydrogen bond term along with the electrostatic term.
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Affiliation(s)
- Arslan R Shaimardanov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Dmitry A Shulga
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Vladimir A Palyulin
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russian Federation
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6
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Cai H, Zhang X, Ling D, Zhang M, Pang C, Chen Z, Jin Z, Ren SC, Chi YR. Discovery of Pyridyl-Benzothiazol Hybrids as Novel Protoporphyrinogen Oxidase Inhibitors via Scaffold Hopping. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 38593435 DOI: 10.1021/acs.jafc.3c08596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
In order to discover novel protoporphyrinogen oxidase (PPO) inhibitors with excellent herbicidal activity, a series of structurally novel 6-(pyridin-2-yl) benzothiazole derivatives were designed based on the scaffold hopping strategy. The in vitro experiments demonstrated that the newly synthesized compounds exhibited noteworthy inhibitory activity against Arabidopsis thaliana PPO (AtPPO), with IC50 values ranging from 0.06 to 1.36 μM. Preliminary postemergence herbicidal activity tests and crop safety studies indicated that some of our compounds exhibited excellent herbicidal activity and crop safety. For instance, compound (rac)-7as exhibited superior herbicidal activities to commercially available flumioxazin (FLU) and saflufenacil (SAF) at all the tested concentrations and showed effective herbicidal activities even at a dosage as low as 18.75 g ai/ha. Meanwhile, compound (rac)-7as showed good crop safety for wheat at a dosage as high as 150 g of ai/ha. Although the absolute configuration of compound 7as has no obvious effect on its herbicidal activity, compound (R)-7as showed a slightly higher crop safety than compound (S)-7as. Molecular simulation studies of Nicotiana tabacum PPO (NtPPO) and our candidate compounds showed that the benzothiazole moiety of compounds (R)-7as or (S)-7as formed multiple π-π stacking interactions with FAD, and the pyridine ring generated π-π stacking with Phe-392. Our finding proved that the pyridyl-benzothiazol hybrids are promising scaffolds for the development of PPO-inhibiting herbicides.
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Affiliation(s)
- Hui Cai
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Xiao Zhang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Dan Ling
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Meng Zhang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Chen Pang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Zhongyin Chen
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Zhichao Jin
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Shi-Chao Ren
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Yonggui Robin Chi
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
- School of Chemistry, Chemical Engineering, and Biotechnology, Nanyang Technological University, Singapore 637371, Singapore
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7
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Akabane T, Suzuki N, Ikeda K, Yonezawa T, Nagatoishi S, Matsumura H, Yoshizawa T, Tsuchiya W, Kamino S, Tsumoto K, Ishimaru K, Katoh E, Hirotsu N. THOUSAND-GRAIN WEIGHT 6, which is an IAA-glucose hydrolase, preferentially recognizes the structure of the indole ring. Sci Rep 2024; 14:6778. [PMID: 38514802 PMCID: PMC10958001 DOI: 10.1038/s41598-024-57506-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 03/19/2024] [Indexed: 03/23/2024] Open
Abstract
An indole-3-acetic acid (IAA)-glucose hydrolase, THOUSAND-GRAIN WEIGHT 6 (TGW6), negatively regulates the grain weight in rice. TGW6 has been used as a target for breeding increased rice yield. Moreover, the activity of TGW6 has been thought to involve auxin homeostasis, yet the details of this putative TGW6 activity remain unclear. Here, we show the three-dimensional structure and substrate preference of TGW6 using X-ray crystallography, thermal shift assays and fluorine nuclear magnetic resonance (19F NMR). The crystal structure of TGW6 was determined at 2.6 Å resolution and exhibited a six-bladed β-propeller structure. Thermal shift assays revealed that TGW6 preferably interacted with indole compounds among the tested substrates, enzyme products and their analogs. Further analysis using 19F NMR with 1,134 fluorinated fragments emphasized the importance of indole fragments in recognition by TGW6. Finally, docking simulation analyses of the substrate and related fragments in the presence of TGW6 supported the interaction specificity for indole compounds. Herein, we describe the structure and substrate preference of TGW6 for interacting with indole fragments during substrate recognition. Uncovering the molecular details of TGW6 activity will stimulate the use of this enzyme for increasing crop yields and contributes to functional studies of IAA glycoconjugate hydrolases in auxin homeostasis.
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Affiliation(s)
- Tatsuki Akabane
- Graduate School of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura, Oura, Gunma, 374-0193, Japan
| | - Nobuhiro Suzuki
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Kazuyoshi Ikeda
- Medicinal Chemistry Data Intelligence Unit, Drug Development Data Intelligence Platform Group, Medical Sciences Innovation Hub Program (MIH), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- Division of Physics for Life Functions, Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen Minato-ku, Tokyo, 105-8512, Japan
| | - Tomoki Yonezawa
- Division of Physics for Life Functions, Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen Minato-ku, Tokyo, 105-8512, Japan
| | - Satoru Nagatoishi
- School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Hiroyoshi Matsumura
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga, 525-8577, Japan
| | - Takuya Yoshizawa
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga, 525-8577, Japan
| | - Wataru Tsuchiya
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Satoshi Kamino
- CRYO SHIP Incorporated, 1-266-3, Sakuragi-cho, Omiya-ku, Saitama, Saitama, 330-0854, Japan
| | - Kouhei Tsumoto
- School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Ken Ishimaru
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Etsuko Katoh
- Department of Food and Nutritional Sciences, Toyo University, 1-1-1 Izumino, Itakura, Oura, Gunma, 374-0193, Japan.
| | - Naoki Hirotsu
- Graduate School of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura, Oura, Gunma, 374-0193, Japan.
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8
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Czestkowski W, Krzemiński Ł, Piotrowicz MC, Mazur M, Pluta E, Andryianau G, Koralewski R, Matyszewski K, Olejniczak S, Kowalski M, Lisiecka K, Kozieł R, Piwowar K, Papiernik D, Nowotny M, Napiórkowska-Gromadzka A, Nowak E, Niedziałek D, Wieczorek G, Siwińska A, Rejczak T, Jędrzejczak K, Mulewski K, Olczak J, Zasłona Z, Gołębiowski A, Drzewicka K, Bartoszewicz A. Structure-Based Discovery of High-Affinity Small Molecule Ligands and Development of Tool Probes to Study the Role of Chitinase-3-Like Protein 1. J Med Chem 2024; 67:3959-3985. [PMID: 38427954 DOI: 10.1021/acs.jmedchem.3c02255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
Chitinase-3-like-1 (CHI3L1), also known as YKL-40, is a glycoprotein linked to inflammation, fibrosis, and cancer. This study explored CHI3L1's interactions with various oligosaccharides using microscale thermophoresis (MST) and AlphaScreen (AS). These investigations guided the development of high-throughput screening assays to assess interference of small molecules in binding between CHI3L1 and biotinylated small molecules or heparan sulfate-based probes. Small molecule binders of YKL-40 were identified in our chitotriosidase inhibitors library with MST and confirmed through X-ray crystallography. Based on cocrystal structures of potent hit compounds with CHI3L1, small molecule probes 19 and 20 were designed for an AS assay. Structure-based optimization led to compounds 30 and 31 with nanomolar activities and drug-like properties. Additionally, an orthogonal AS assay using biotinylated heparan sulfate as a probe was developed. The compounds' affinity showed a significant correlation in both assays. These screening tools and compounds offer novel avenues for investigating the role of CHI3L1.
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Affiliation(s)
| | | | | | - Marzena Mazur
- Molecure S.A., Żwirki I Wigury 101, Warsaw 02-089, Poland
| | - Elżbieta Pluta
- Molecure S.A., Żwirki I Wigury 101, Warsaw 02-089, Poland
| | | | | | | | | | | | | | - Rafał Kozieł
- Molecure S.A., Żwirki I Wigury 101, Warsaw 02-089, Poland
| | | | | | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology in Warsaw, Ks. Trojdena 4, Warsaw 02-109, Poland
| | - Agnieszka Napiórkowska-Gromadzka
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology in Warsaw, Ks. Trojdena 4, Warsaw 02-109, Poland
| | - Elżbieta Nowak
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology in Warsaw, Ks. Trojdena 4, Warsaw 02-109, Poland
| | | | | | - Anna Siwińska
- Molecure S.A., Żwirki I Wigury 101, Warsaw 02-089, Poland
| | - Tomasz Rejczak
- Molecure S.A., Żwirki I Wigury 101, Warsaw 02-089, Poland
| | | | | | - Jacek Olczak
- Molecure S.A., Żwirki I Wigury 101, Warsaw 02-089, Poland
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9
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Vu NP, Ali L, Chua TL, Barr DA, Hendrickson HP, Trivedi DJ. Computational Insights into Prostaglandin E 2 Ligand Binding and Activation of G-Protein-Coupled Receptors. ACS APPLIED BIO MATERIALS 2024; 7:579-587. [PMID: 37058420 DOI: 10.1021/acsabm.2c01049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
G-protein coupled receptors (GPCRs) are eukaryotic integral membrane proteins that regulate signal transduction cascade pathways implicated in a variety of human diseases and are consequently of interest as drug targets. For this reason, it is of interest to investigate the way in which specific ligands bind and trigger conformational changes in the receptor during activation and how this in turn modulates intracellular signaling. In the present study, we investigate the way in which the ligand Prostaglandin E2 interacts with three GPCRs in the E-prostanoid family: EP1, EP2, and EP3. We examine information transfer pathways based on long-time scale molecular dynamics simulations using transfer entropy and betweenness centrality to measure the physical transfer of information among residues in the system. We monitor specific residues involved in binding to the ligand and investigate how the information transfer behavior of these residues changes upon ligand binding. Our results provide key insights that enable a deeper understanding of EP activation and signal transduction functioning pathways at the molecular level, as well as enabling us to make some predictions about the activation pathway for the EP1 receptor, for which little structural information is currently available. Our results should advance ongoing efforts in the development of potential therapeutics targeting these receptors.
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Affiliation(s)
- Nam P Vu
- Department of Chemistry, Lafayette College, Easton, Pennsylvania 18042, United States
| | - Luke Ali
- Department of Physics, Clarkson University, Potsdam, New York 13699, United States
| | - Theresa L Chua
- Department of Chemistry, Lafayette College, Easton, Pennsylvania 18042, United States
| | - Daniel A Barr
- Department of Chemistry, University of Mary, Bismarck, North Dakota 58504, United States
| | - Heidi P Hendrickson
- Department of Chemistry, Lafayette College, Easton, Pennsylvania 18042, United States
| | - Dhara J Trivedi
- Department of Physics, Clarkson University, Potsdam, New York 13699, United States
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10
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Liu J, Li Y, Wang P, Zhang Y, Tian Z. High-efficiency removal of pyrethroids using a redesigned odorant binding protein. JOURNAL OF HAZARDOUS MATERIALS 2024; 463:132856. [PMID: 37913660 DOI: 10.1016/j.jhazmat.2023.132856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/16/2023] [Accepted: 10/23/2023] [Indexed: 11/03/2023]
Abstract
Pyrethroids are ubiquitously present in environmental media and threaten both the ecosystem and human health. To explore effective ways to remove pyrethroids from the environment, an odorant binding protein (OBP) with affinity for various pyrethroids was investigated. Initially, the target OBP, Spodoptera littoralis pheromone binding protein 1 (SlitPBP1), underwent redesign to enhance its affinity for pyrethroids. The modified SlitPBP1E97ND106E demonstrated a substantially increased affinity for deltamethrin (DeltaM), with a dissociation constant of 0.77 ± 0.17 μM. The affinity of SlitPBP1E97ND106E for other pyrethroids also increased to varying extents. Consequently, SlitPBP1E97ND106E displayed a markedly enhanced capability to adsorb and remove pyrethroids. When exposed to free SlitPBP1E97ND106E in solution, the reduction in DeltaM surged from 16.78 ± 0.32% to 97.51 ± 0.56%. SlitPBP1E97ND106E was immobilized by coupling the protein to Ni2+-NTA agarose resin. Liquid chromatography results attested to the superior efficacy of immobilized SlitPBP1E97ND106E in removing pyrethroids, especially DeltaM. No significant differences in pyrethroid removal were detected across various water samples. Our findings introduce a potent tool for pyrethroid removal. A wider range of OBPs can similarly be optimized and applied to remove organic pollutants, including but not limited to pesticides.
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Affiliation(s)
- Jiyuan Liu
- Key Laboratory of Plant Protection Resources & Pest Management of the Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yifan Li
- Key Laboratory of Plant Protection Resources & Pest Management of the Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Pei Wang
- Key Laboratory of Plant Protection Resources & Pest Management of the Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yalin Zhang
- Key Laboratory of Plant Protection Resources & Pest Management of the Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Zhen Tian
- Key Laboratory of Plant Protection Resources & Pest Management of the Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China.
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11
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Girase R, Ahmad I, Patel H. Bioisosteric modification of Linezolid identified the potential M. tuberculosis protein synthesis inhibitors to overcome the myelosuppression and serotonergic toxicity associated with Linezolid in the treatment of the multi-drug resistance tuberculosis (MDR-TB). J Biomol Struct Dyn 2024; 42:2111-2126. [PMID: 37097976 DOI: 10.1080/07391102.2023.2203254] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 04/10/2023] [Indexed: 04/26/2023]
Abstract
Linezolid is the first and only oxazolidinone antibacterial drug was approved in the last 35 years. It exhibits bacteriostatic efficacy against M. tuberculosis and is a crucial constituent of the BPaL regimen (Bedaquiline, Pretomanid, and Linezolid), which was authorized by the FDA in 2019 for the treatment of XDR-TB or MDR-TB. Despite its unique mechanism of action, Linezolid carries a considerable risk of toxicity, including myelosuppression and serotonin syndrome (SS), which is caused by inhibition of mitochondrial protein synthesis (MPS) and monoamine oxidase (MAO), respectively. Based on the structure toxicity relationship (STR) of Linezolid, in this work, we used a bioisosteric replacement approach to optimize the structure of Linezolid at the C-ring and/or C-5 position for myelosuppression and serotogenic toxicity. Extensive hierarchical multistep docking, drug likeness prediction, molecular binding interactions analyses, and toxicity assessment identified three promising compounds (3071, 7549 and 9660) as less toxic potential modulators of Mtb EthR protein. Compounds 3071, 7549 and 9660 were having the significant docking score of -12.696 Kcal/mol, -12.681 Kcal/mol and -15.293 Kcal/mol towards the Mtb EthR protein with less MAO-A and B affinity [compound 3071: MAO A (-4.799 Kcal/mol) and MAO B (-6.552 Kcal/mol); compound 7549: MAO A (> -2.00 Kcal/mol) and MAO B (> -2.00 Kcal/mol) and compound 9660: MAO A (> -5.678 Kcal/mol) and MAO B (> -6.537Kcal/mol) and none of them shown the Leukopenia as a side effect due to the Myelosuppression. The MD simulation results and binding free energy estimations correspond well with docking analyses, indicating that the proposed compounds bind and inhibit the EthR protein more effectively than Linezolid. The quantum mechanical and electrical characteristics were evaluated using density functional theory (DFT), which also demonstrated that the proposed compounds are more reactive than Linezolid.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rukaiyya Girase
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, India
| | - Iqrar Ahmad
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, India
| | - Harun Patel
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, India
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12
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Napolitano C, Benfatti F, Hamdan FB, Bristow JA, Dapiaggi F, Firth LC, Guest M, Saunders HA, Hall RG, Monaco MR, Quetglas V, Rendine S, Eterovic M. Synthesis and insecticidal activity of N-(5-phenylpyrazin-2-yl)-benzamide derivatives: Elucidation of mode of action on chitin biosynthesis through symptomology and genetic studies. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2024; 199:105771. [PMID: 38458679 DOI: 10.1016/j.pestbp.2024.105771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/17/2023] [Accepted: 01/08/2024] [Indexed: 03/10/2024]
Abstract
Among the six-membered heterocycles, the pyrazine ring is poorly explored in crop protection and does not feature in any product listed in the current IRAC MoA classification. In an effort to identify new leads for internal research, we synthesized a series of N-(5-phenylpyrazin-2-yl)-benzamide derivatives and evaluated them for their insecticidal activity. N-(5-phenylpyrazin-2-yl)-benzamide derivatives 3 were prepared using an automated two-step synthesis protocol. These compounds were tested for their initial biological activity against a wide range of sucking and chewing insect pests and found to be active against lepidopterans only. More detailed experiments, including symptomology studies on the diamondback moth, Plutella xylostella (L.) and the Egyptian cotton leafworm, Spodoptera littoralis (Boisduval) showed that analog 3q causes severe abnormalities in the lepidopteran cuticle leading to larval mortality. Compound 3q shows strong potency against both P. xylostella and S. littoralis, whereas analog 3i shows better potency against S. littoralis causing also impaired cuticular structure and death of the larvae. Additionally, P. xylostella genetic studies showed that compound 3q resistance is linked to Chitin Synthase 1. Our studies show that N-(5-phenylpyrazin-2-yl)-benzamide derivatives 3, and in particular analogs 3i and 3q, act as insect growth modulator insecticides. Conformational similarities with lufenuron are discussed.
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Affiliation(s)
- Carmela Napolitano
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, Stein CH-4332, Switzerland
| | - Fides Benfatti
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, Stein CH-4332, Switzerland
| | - Farhan Bou Hamdan
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, Stein CH-4332, Switzerland
| | - Julia A Bristow
- Syngenta Crop Protection, Jealott's Hill International Research Centre, Bracknell, Berkshire RG42 6EY, UK
| | - Federico Dapiaggi
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, Stein CH-4332, Switzerland
| | - Lucy C Firth
- Syngenta Crop Protection, Jealott's Hill International Research Centre, Bracknell, Berkshire RG42 6EY, UK
| | - Marcus Guest
- Syngenta Crop Protection, Jealott's Hill International Research Centre, Bracknell, Berkshire RG42 6EY, UK.
| | - Helena A Saunders
- Syngenta Crop Protection, Jealott's Hill International Research Centre, Bracknell, Berkshire RG42 6EY, UK
| | - Roger G Hall
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, Stein CH-4332, Switzerland
| | - Mattia R Monaco
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, Stein CH-4332, Switzerland
| | - Vincent Quetglas
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, Stein CH-4332, Switzerland
| | - Stefano Rendine
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, Stein CH-4332, Switzerland
| | - Marisa Eterovic
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, Stein CH-4332, Switzerland.
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13
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Miciaccia M, Rizzo F, Centonze A, Cavallaro G, Contino M, Armenise D, Baldelli OM, Solidoro R, Ferorelli S, Scarcia P, Agrimi G, Zingales V, Cimetta E, Ronsisvalle S, Sipala FM, Polosa PL, Fortuna CG, Perrone MG, Scilimati A. Harmaline to Human Mitochondrial Caseinolytic Serine Protease Activation for Pediatric Diffuse Intrinsic Pontine Glioma Treatment. Pharmaceuticals (Basel) 2024; 17:135. [PMID: 38276008 PMCID: PMC10821046 DOI: 10.3390/ph17010135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/09/2024] [Accepted: 01/15/2024] [Indexed: 01/27/2024] Open
Abstract
Diffuse intrinsic pontine glioma (DIPG), affecting children aged 4-7 years, is a rare, aggressive tumor that originates in the pons and then spreads to nearby tissue. DIPG is the leading cause of death for pediatric brain tumors due to its infiltrative nature and inoperability. Radiotherapy has only a palliative effect on stabilizing symptoms. In silico and preclinical studies identified ONC201 as a cytotoxic agent against some human cancer cell lines, including DIPG ones. A single-crystal X-ray analysis of the complex of the human mitochondrial caseinolytic serine protease type C (hClpP) and ONC201 (PDB ID: 6DL7) allowed hClpP to be identified as its main target. The hyperactivation of hClpP causes damage to mitochondrial oxidative phosphorylation and cell death. In some DIPG patients receiving ONC201, an acquired resistance was observed. In this context, a wide program was initiated to discover original scaffolds for new hClpP activators to treat ONC201-non-responding patients. Harmaline, a small molecule belonging to the chemical class of β-carboline, was identified through Fingerprints for Ligands and Proteins (FLAP), a structure-based virtual screening approach. Molecular dynamics simulations and a deep in vitro investigation showed interesting information on the interaction and activation of hClpP by harmaline.
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Affiliation(s)
- Morena Miciaccia
- Research Laboratory for Woman and Child Health, Department of Pharmacy-Pharmaceutical Sciences, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (M.M.); (A.C.); (D.A.); (O.M.B.); (R.S.); (S.F.)
| | - Francesca Rizzo
- Department of Biosciences, Biotechnologies, and Environment, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (F.R.); (P.S.); (G.A.); (P.L.P.)
| | - Antonella Centonze
- Research Laboratory for Woman and Child Health, Department of Pharmacy-Pharmaceutical Sciences, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (M.M.); (A.C.); (D.A.); (O.M.B.); (R.S.); (S.F.)
| | - Gianfranco Cavallaro
- Laboratory of Molecular Modelling and Heterocyclic Compounds ModHet, Department of Chemical Sciences, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy;
| | - Marialessandra Contino
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy;
| | - Domenico Armenise
- Research Laboratory for Woman and Child Health, Department of Pharmacy-Pharmaceutical Sciences, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (M.M.); (A.C.); (D.A.); (O.M.B.); (R.S.); (S.F.)
| | - Olga Maria Baldelli
- Research Laboratory for Woman and Child Health, Department of Pharmacy-Pharmaceutical Sciences, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (M.M.); (A.C.); (D.A.); (O.M.B.); (R.S.); (S.F.)
| | - Roberta Solidoro
- Research Laboratory for Woman and Child Health, Department of Pharmacy-Pharmaceutical Sciences, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (M.M.); (A.C.); (D.A.); (O.M.B.); (R.S.); (S.F.)
| | - Savina Ferorelli
- Research Laboratory for Woman and Child Health, Department of Pharmacy-Pharmaceutical Sciences, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (M.M.); (A.C.); (D.A.); (O.M.B.); (R.S.); (S.F.)
| | - Pasquale Scarcia
- Department of Biosciences, Biotechnologies, and Environment, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (F.R.); (P.S.); (G.A.); (P.L.P.)
| | - Gennaro Agrimi
- Department of Biosciences, Biotechnologies, and Environment, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (F.R.); (P.S.); (G.A.); (P.L.P.)
| | - Veronica Zingales
- Department of Industrial Engineering (DII), University of Padua, Via Marzolo 9, 35131 Padova, Italy; (V.Z.); (E.C.)
| | - Elisa Cimetta
- Department of Industrial Engineering (DII), University of Padua, Via Marzolo 9, 35131 Padova, Italy; (V.Z.); (E.C.)
| | - Simone Ronsisvalle
- Department of Drug and Health Sciences, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy; (S.R.); (F.M.S.)
| | - Federica Maria Sipala
- Department of Drug and Health Sciences, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy; (S.R.); (F.M.S.)
| | - Paola Loguercio Polosa
- Department of Biosciences, Biotechnologies, and Environment, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (F.R.); (P.S.); (G.A.); (P.L.P.)
| | - Cosimo Gianluca Fortuna
- Laboratory of Molecular Modelling and Heterocyclic Compounds ModHet, Department of Chemical Sciences, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy;
| | - Maria Grazia Perrone
- Research Laboratory for Woman and Child Health, Department of Pharmacy-Pharmaceutical Sciences, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (M.M.); (A.C.); (D.A.); (O.M.B.); (R.S.); (S.F.)
| | - Antonio Scilimati
- Research Laboratory for Woman and Child Health, Department of Pharmacy-Pharmaceutical Sciences, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (M.M.); (A.C.); (D.A.); (O.M.B.); (R.S.); (S.F.)
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14
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Herz AM, Kellici T, Morao I, Michel J. Alchemical Free Energy Workflows for the Computation of Protein-Ligand Binding Affinities. Methods Mol Biol 2024; 2716:241-264. [PMID: 37702943 DOI: 10.1007/978-1-0716-3449-3_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
Alchemical free energy methods can be used for the efficient computation of relative binding free energies during preclinical drug discovery stages. In recent years, this has been facilitated further by the implementation of workflows that enable non-experts to quickly and consistently set up the required simulations. Given the correct input structures, workflows handle the difficult aspects of setting up perturbations, including consistently defining the perturbable molecule, its atom mapping and topology generation, perturbation network generation, running of the simulations via different sampling methods, and analysis of the results. Different academic and commercial workflows are discussed, including FEW, FESetup, FEPrepare, CHARMM-GUI, Transformato, PMX, QLigFEP, TIES, ProFESSA, PyAutoFEP, BioSimSpace, FEP+, Flare, and Orion. These workflows differ in various aspects, such as mapping algorithms or enhanced sampling methods. Some workflows can accommodate more than one molecular dynamics (MD) engine and use external libraries for tasks. Differences between workflows can present advantages for different use cases, however a lack of interoperability of the workflows' components hinders systematic comparisons.
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Affiliation(s)
- Anna M Herz
- EaStChem School of Chemistry, Joseph Black Building, University of Edinburgh, Edinburgh, UK
| | - Tahsin Kellici
- Evotec (UK) Ltd., In Silico Research and Development, Abingdon, Oxfordshire, UK
- Merck & Co., Inc., Modelling and Informatics, West Point, PA, USA
| | - Inaki Morao
- Evotec (UK) Ltd., In Silico Research and Development, Abingdon, Oxfordshire, UK
| | - Julien Michel
- EaStChem School of Chemistry, Joseph Black Building, University of Edinburgh, Edinburgh, UK.
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15
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Wu J, Lv J, Zhao L, Zhao R, Gao T, Xu Q, Liu D, Yu Q, Ma F. Exploring the role of microbial proteins in controlling environmental pollutants based on molecular simulation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167028. [PMID: 37704131 DOI: 10.1016/j.scitotenv.2023.167028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 09/03/2023] [Accepted: 09/10/2023] [Indexed: 09/15/2023]
Abstract
Molecular simulation has been widely used to study microbial proteins' structural composition and dynamic properties, such as volatility, flexibility, and stability at the microscopic scale. Herein, this review describes the key elements of molecular docking and molecular dynamics (MD) simulations in molecular simulation; reviews the techniques combined with molecular simulation, such as crystallography, spectroscopy, molecular biology, and machine learning, to validate simulation results and bridge information gaps in the structure, microenvironmental changes, expression mechanisms, and intensity quantification; illustrates the application of molecular simulation, in characterizing the molecular mechanisms of interaction of microbial proteins with four different types of contaminants, namely heavy metals (HMs), pesticides, dyes and emerging contaminants (ECs). Finally, the review outlines the important role of molecular simulations in the study of microbial proteins for controlling environmental contamination and provides ideas for the application of molecular simulation in screening microbial proteins and incorporating targeted mutagenesis to obtain more effective contaminant control proteins.
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Affiliation(s)
- Jieting Wu
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Jin Lv
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Lei Zhao
- State Key Laboratory of Urban Water Resources & Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Ruofan Zhao
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Tian Gao
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, China
| | - Qi Xu
- PetroChina Fushun Petrochemical Company, Fushun 113000, China
| | - Dongbo Liu
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Qiqi Yu
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Fang Ma
- State Key Laboratory of Urban Water Resources & Environment, Harbin Institute of Technology, Harbin 150090, China.
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16
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Pacalon J, Audic G, Magnat J, Philip M, Golebiowski J, Moreau CJ, Topin J. Elucidation of the structural basis for ligand binding and translocation in conserved insect odorant receptor co-receptors. Nat Commun 2023; 14:8182. [PMID: 38081900 PMCID: PMC10713630 DOI: 10.1038/s41467-023-44058-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
In numerous insects, the olfactory receptor family forms a unique class of heteromeric cation channels. Recent progress in resolving the odorant receptor structures offers unprecedented opportunities for deciphering their molecular mechanisms of ligand recognition. Unexpectedly, these structures in apo or ligand-bound states did not reveal the pathway taken by the ligands between the extracellular space and the deep internal cavities. By combining molecular modeling with electrophysiological recordings, we identified amino acids involved in the dynamic entry pathway and the binding of VUAA1 to Drosophila melanogaster's odorant receptor co-receptor (Orco). Our results provide evidence for the exact location of the agonist binding site and a detailed and original mechanism of ligand translocation controlled by a network of conserved residues. These findings would explain the particularly high selectivity of Orcos for their ligands.
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Affiliation(s)
- Jody Pacalon
- Université Côte d'Azur, Institut de Chimie de Nice UMR7272, CNRS, Nice, France
| | | | | | - Manon Philip
- Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Jérôme Golebiowski
- Department of Brain & Cognitive Sciences, DGIST, 333, Techno JungAng, Daero, HyeongPoong Myeon, Daegu, Republic of Korea
| | | | - Jérémie Topin
- Université Côte d'Azur, Institut de Chimie de Nice UMR7272, CNRS, Nice, France.
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17
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Raju B, Sapra B, Silakari O. 3D-QSAR assisted identification of selective CYP1B1 inhibitors: an effective bioisosteric replacement/molecular docking/electrostatic complementarity analysis. Mol Divers 2023; 27:2673-2693. [PMID: 36441444 DOI: 10.1007/s11030-022-10574-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/20/2022] [Indexed: 11/29/2022]
Abstract
Cytochrome P450-1B1 is a majorly overexpressed drug-metabolizing enzyme in tumors and is responsible for inactivation and subsequent resistance to a variety of anti-cancer drugs, i.e., docetaxel, tamoxifen, and cisplatin. In the present study, a 3D quantitative structure-activity relationship (3D-QSAR) model has been constructed for the identification, design, and optimization of novel CYP1B1 inhibitors. The model has been built using a set of 148 selective CYP1B1 inhibitors. The developed model was evaluated based on certain statistical parameters including q2 and r2 which showed the acceptable predictive and descriptive capability of the generated model. The developed 3D-QSAR model assisted in understanding the key molecular fields which were firmly related to the selective CYP1B1 inhibition. A theoretic approach for the generation of new lead compounds with optimized CYP1B1 receptor affinity has been performed utilizing bioisosteric replacement analysis. These generated molecules were subjected to a developed 3D-QSAR model to predict the inhibitory activity potentials. Furthermore, these compounds were scrutinized through the activity atlas model, molecular docking, electrostatic complementarity, molecular dynamics, and waterswap analysis. The final hits might act as selective CYP1B1 inhibitors which could address the issue of resistance. This 3D-QSAR includes several chemically diverse selective CYP1B1 receptor ligands and well accounts for the individual ligand's inhibition affinities. These features of the developed 3D-QSAR model will ensure future prospective applications of the model to speed up the identification of new potent and selective CYP1B1 receptor ligands.
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Affiliation(s)
- Baddipadige Raju
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, India
| | - Bharti Sapra
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, India
| | - Om Silakari
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, India.
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18
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Wojtala D, Kozieł S, Witwicki M, Niorettini A, Guz-Regner K, Bugla-Płoskońska G, Caramori S, Komarnicka UK. Antibactericidal Ir(III) and Ru(II) Complexes with Phosphine-Alkaloid Conjugate and Their Interactions with Biomolecules: A Case of N-Methylphenethylamine. Chemistry 2023; 29:e202301603. [PMID: 37584222 DOI: 10.1002/chem.202301603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 08/06/2023] [Accepted: 08/15/2023] [Indexed: 08/17/2023]
Abstract
The phosphine ligand (Ph2 PCH2 N(CH3 )(CH2 )2 Ph, PNMPEA) obtained by the reaction of the (hydroxymethyl)diphenylphosphine with naturally occurring alkaloid N-methylphenethylamine, was used to synthesize the half-sandwich iridium(III) (Ir(η5 -Cp*)Cl2 Ph2 PCH2 N(CH3 )(CH2 )2 Ph, IrPNMPEA) and ruthenium(II) (Ru(η6 -p-cymene)Cl2 Ph2 PCH2 N(CH3 )(CH2 )2 Ph, RuPNMPEA) complexes. They were characterized using a vast array of methods, including 1D and 2D NMR, ESI(+)MS spectrometry, elemental analysis, cyclic voltammetry (CV), electron spectroscopy in the UV-Vis range (absorption, fluorescence) and density functional theory (DFT). The initial antimicrobial activity in vitro toward Gram-positive and Gram-negative bacterial strains was examined, indicating that both complexes are selective towards Gram-positive bacteria, e. g., Staphylococcus aureus, where the IrPNMPEA has been more bactericidal compared to RuPNMPEA. Additionally, the interactions of these compounds with various biomolecules, such as DNA (ctDNA, plasmid DNA, 9-ethylguanine (9-EtG), and 9-methyladenine (9-MeA)), nicotinamide adenine dinucleotide (NADH), glutathione (GSH), and ascorbic acid (Asc) were described. The results showed that both Ir(III) and Ru(II) complexes accelerate the oxidation process of NADH, GSH and Asc that appeared to occur by an electron transfer mechanism. Interestingly, only IrPNMPEA leads to the formation of various biomolecule adducts, which can explain its higher activity. Furthermore, RuPNMPEA and IrPNMPEA have been interacting with the DNA through weak noncovalent interactions.
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Affiliation(s)
- Daria Wojtala
- Faculty of Chemistry, University of Wroclaw, Joliot-Curie 14, 50-383, Wroclaw, Poland
| | - Sandra Kozieł
- Faculty of Chemistry, University of Wroclaw, Joliot-Curie 14, 50-383, Wroclaw, Poland
| | - Maciej Witwicki
- Faculty of Chemistry, University of Wroclaw, Joliot-Curie 14, 50-383, Wroclaw, Poland
| | - Alessandro Niorettini
- Department of Chemical, Pharmaceutical, and Agricultural Sciences, University of Ferrara, Via L. Borsari 46, 44121, Ferrara, Italy
| | - Katarzyna Guz-Regner
- Department of Microbiology, Faculty of Biological Sciences, University of Wroclaw, Przybyszewskiego 63-77, 51-148, Wroclaw, Poland
| | - Gabriela Bugla-Płoskońska
- Department of Microbiology, Faculty of Biological Sciences, University of Wroclaw, Przybyszewskiego 63-77, 51-148, Wroclaw, Poland
| | - Stefano Caramori
- Department of Chemical, Pharmaceutical, and Agricultural Sciences, University of Ferrara, Via L. Borsari 46, 44121, Ferrara, Italy
| | - Urszula K Komarnicka
- Faculty of Chemistry, University of Wroclaw, Joliot-Curie 14, 50-383, Wroclaw, Poland
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19
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Braconi L, Dei S, Contino M, Riganti C, Bartolucci G, Manetti D, Romanelli MN, Perrone MG, Colabufo NA, Guglielmo S, Teodori E. Tetrazole and oxadiazole derivatives as bioisosteres of tariquidar and elacridar: New potent P-gp modulators acting as MDR reversers. Eur J Med Chem 2023; 259:115716. [PMID: 37573829 DOI: 10.1016/j.ejmech.2023.115716] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/22/2023] [Accepted: 08/07/2023] [Indexed: 08/15/2023]
Abstract
New 2,5- and 1,5-disubstituted tetrazoles, and 2,5-disubstituted-1,3,4-oxadiazoles were synthesized as tariquidar and elacridar derivatives and studied as multidrug resistance (MDR) reversers. Their behaviour on the three ABC transporters P-gp, MRP1 and BCRP was investigated. All compounds inhibited the P-gp transport activity in MDCK-MDR1 cells overexpressing P-gp, showing EC50 values even in the low nanomolar range (compounds 15, 22). Oxadiazole derivatives were able to increase the antiproliferative effect of doxorubicin in MDCK-MDR1 and in HT29/DX cells confirming their nature of P-gp modulators, with derivative 15 being the most potent in these assays. Compound 15 also displayed a dual inhibitory effect showing good activities towards both P-gp and BCRP. A computational study suggested a common interaction pattern on P-gp for most of the potent compounds. The bioisosteric substitution of the amide group of lead compounds allowed identifying a new set of potent oxadiazole derivatives that modulate MDR through inhibition of the P-gp efflux activity. If compared to previous amide derivatives, the introduction of the heterocycle rings greatly enhances the activity on P-gp, introduces in two compounds a moderate inhibitory activity on MRP1 and maintains in some cases the effect on BCRP, leading to the unveiling of dual inhibitor 15.
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Affiliation(s)
- Laura Braconi
- Department of Neuroscience, Psychology, Drug Research and Child Health - Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Via Ugo Schiff 6, 50019, Sesto Fiorentino, Italy
| | - Silvia Dei
- Department of Neuroscience, Psychology, Drug Research and Child Health - Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Via Ugo Schiff 6, 50019, Sesto Fiorentino, Italy.
| | - Marialessandra Contino
- Department of Pharmacy - Drug Sciences, University of Bari "A. Moro", via Orabona 4, 70125, Bari, Italy
| | - Chiara Riganti
- Department of Oncology, University of Turin, Via Santena 5/bis, 10126, Torino, Italy
| | - Gianluca Bartolucci
- Department of Neuroscience, Psychology, Drug Research and Child Health - Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Via Ugo Schiff 6, 50019, Sesto Fiorentino, Italy
| | - Dina Manetti
- Department of Neuroscience, Psychology, Drug Research and Child Health - Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Via Ugo Schiff 6, 50019, Sesto Fiorentino, Italy
| | - Maria Novella Romanelli
- Department of Neuroscience, Psychology, Drug Research and Child Health - Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Via Ugo Schiff 6, 50019, Sesto Fiorentino, Italy
| | - Maria Grazia Perrone
- Department of Pharmacy - Drug Sciences, University of Bari "A. Moro", via Orabona 4, 70125, Bari, Italy
| | - Nicola Antonio Colabufo
- Department of Pharmacy - Drug Sciences, University of Bari "A. Moro", via Orabona 4, 70125, Bari, Italy
| | - Stefano Guglielmo
- Department of Drug Science and Technology, University of Turin, Via P. Giuria 9, 10125, Torino, Italy
| | - Elisabetta Teodori
- Department of Neuroscience, Psychology, Drug Research and Child Health - Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Via Ugo Schiff 6, 50019, Sesto Fiorentino, Italy
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20
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Ruengsatra T, Meeprasert A, Rattanangkool E, Deesiri S, Srisa J, Udomnilobol U, Dunkoksung W, Chuaypen N, Kiatbumrung R, Tangkijvanich P, Vimolmangkang S, Pudhom K, Prueksaritanont T. Binding characteristics of pyrrole-scaffold hepatitis B virus capsid inhibitors and identification of novel potent compounds. RSC Adv 2023; 13:29004-29022. [PMID: 37807973 PMCID: PMC10556424 DOI: 10.1039/d3ra04720b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/24/2023] [Indexed: 10/10/2023] Open
Abstract
Hepatitis B virus (HBV) capsid assembly modulators (CAMs) are currently being evaluated in clinical trials as potential curative therapies for HBV. This study used in silico computational modeling to provide insights into the binding characteristics between the HBV core protein and two pyrrole-scaffold inhibitors, JNJ-6379 and GLP-26, both in the CAM-Normal (CAM-N) series. Molecular dynamics simulations showed that the pyrrole inhibitors displayed similar general binding-interaction patterns to NVR 3-778, another CAM-N, with hydrophobic interactions serving as the major driving force. However, consistent with their higher potency, the pyrrole inhibitors exhibited stronger nonpolar interactions with key residues in a solvent-accessible region as compared to NVR 3-778. This feature was facilitated by distinct hydrogen bond interactions of the pyrrole scaffold inhibitors with the residue 140 in chain B of the HBV core protein (L140B). Based on these findings, novel CAM-N compounds were designed to mimic the interaction with L140B residue while maximizing nonpolar interactions in the solvent-accessible region. Several 1H-pyrrole-2-carbonyl substituted pyrrolidine-based compounds with various hydrophobic side chains were synthesized and evaluated. Through analyses of the structure-activity and structure-druggability relations of a series of compounds, CU15 emerged as the most promising lead CAM-N compound, exhibiting sub-nanomolar potency and good pharmacokinetic profiles. Overall, the study demonstrated a practical approach to leverage computational methods for understanding key target binding features for rationale-based design, and for guiding the identification of novel compounds.
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Affiliation(s)
- Tanachote Ruengsatra
- Chulalongkorn University Drug Discovery and Drug Development Research Center (Chula4DR), Chulalongkorn University 254 Phayathai Rd, Prathumwan Bangkok 10330 Thailand
| | - Arthitaya Meeprasert
- Chulalongkorn University Drug Discovery and Drug Development Research Center (Chula4DR), Chulalongkorn University 254 Phayathai Rd, Prathumwan Bangkok 10330 Thailand
| | - Eakkaphon Rattanangkool
- Chulalongkorn University Drug Discovery and Drug Development Research Center (Chula4DR), Chulalongkorn University 254 Phayathai Rd, Prathumwan Bangkok 10330 Thailand
| | - Sirikan Deesiri
- Chulalongkorn University Drug Discovery and Drug Development Research Center (Chula4DR), Chulalongkorn University 254 Phayathai Rd, Prathumwan Bangkok 10330 Thailand
| | - Jakkrit Srisa
- Chulalongkorn University Drug Discovery and Drug Development Research Center (Chula4DR), Chulalongkorn University 254 Phayathai Rd, Prathumwan Bangkok 10330 Thailand
| | - Udomsak Udomnilobol
- Chulalongkorn University Drug Discovery and Drug Development Research Center (Chula4DR), Chulalongkorn University 254 Phayathai Rd, Prathumwan Bangkok 10330 Thailand
| | - Wilasinee Dunkoksung
- Chulalongkorn University Drug Discovery and Drug Development Research Center (Chula4DR), Chulalongkorn University 254 Phayathai Rd, Prathumwan Bangkok 10330 Thailand
| | - Natthaya Chuaypen
- Chulalongkorn University Drug Discovery and Drug Development Research Center (Chula4DR), Chulalongkorn University 254 Phayathai Rd, Prathumwan Bangkok 10330 Thailand
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University Bangkok Thailand
| | - Rattanaporn Kiatbumrung
- Chulalongkorn University Drug Discovery and Drug Development Research Center (Chula4DR), Chulalongkorn University 254 Phayathai Rd, Prathumwan Bangkok 10330 Thailand
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University Bangkok Thailand
| | - Pisit Tangkijvanich
- Chulalongkorn University Drug Discovery and Drug Development Research Center (Chula4DR), Chulalongkorn University 254 Phayathai Rd, Prathumwan Bangkok 10330 Thailand
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University Bangkok Thailand
| | - Sornkanok Vimolmangkang
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University Bangkok Thailand
| | - Khanitha Pudhom
- Department of Chemistry, Faculty of Science, Chulalongkorn University Bangkok Thailand
| | - Thomayant Prueksaritanont
- Chulalongkorn University Drug Discovery and Drug Development Research Center (Chula4DR), Chulalongkorn University 254 Phayathai Rd, Prathumwan Bangkok 10330 Thailand
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21
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Rathje OH, Perryman L, Payne RJ, Hamprecht DW. PROTACs Targeting MLKL Protect Cells from Necroptosis. J Med Chem 2023; 66:11216-11236. [PMID: 37535857 DOI: 10.1021/acs.jmedchem.3c00665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Mixed Lineage Kinase domain-Like pseudokinase (MLKL) is implicated in a broad range of diseases due to its role as the ultimate effector of necroptosis and has therefore emerged as an attractive drug target. Here, we describe the development of PROteolysis TArgeting Chimeras (PROTACs) as a novel approach to knock down MLKL through chemical means. A series of candidate degraders were synthesized from a high-affinity pyrazole carboxamide-based MLKL ligand leading to the identification of a PROTAC molecule that effectively degraded MLKL and completely abrogated cell death in a TSZ model of necroptosis. By leveraging the innate ability of these PROTACs to degrade MLKL in a dose-dependent manner, the quantitative relationship between MLKL levels and necroptosis was interrogated. This work demonstrates the feasibility of targeting MLKL using a PROTAC approach and provides a powerful tool to further our understanding of the role of MLKL within the necroptotic pathway.
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Affiliation(s)
- Oliver H Rathje
- Pharmaxis Ltd., 20 Rodborough Road, Frenchs Forest, NSW 2086, Australia
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Lara Perryman
- Pharmaxis Ltd., 20 Rodborough Road, Frenchs Forest, NSW 2086, Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
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22
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Lomin SN, Kolachevskaya OO, Arkhipov DV, Romanov GA. Canonical and Alternative Auxin Signaling Systems in Mono-, Di-, and Tetraploid Potatoes. Int J Mol Sci 2023; 24:11408. [PMID: 37511169 PMCID: PMC10380454 DOI: 10.3390/ijms241411408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/08/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
It has long been known that the phytohormone auxin plays a promoting role in tuber formation and stress tolerance in potatoes. Our study aimed to identify and characterize the complete sets of auxin-related genes that presumably constitute the entire auxin signaling system in potato (Solanum tuberosum L.). The corresponding genes were retrieved from sequenced genomes of the doubled monoploid S. tuberosum DM1-3-516-R44 (DM) of the Phureja group, the heterozygous diploid line RH89-039-16 (RH), and the autotetraploid cultivar Otava. Both canonical and noncanonical auxin signaling pathways were considered. Phylogenetic and domain analyses of deduced proteins were supplemented by expression profiling and 3D molecular modeling. The canonical and ABP1-mediated pathways of auxin signaling appeared to be well conserved. The total number of potato genes/proteins presumably involved in canonical auxin signaling is 46 and 108 in monoploid DM and tetraploid Otava, respectively. Among the studied potatoes, spectra of expressed genes obviously associated with auxin signaling were partly cultivar-specific and quite different from analogous spectrum in Arabidopsis. Most of the noncanonical pathways found in Arabidopsis appeared to have low probability in potato. This was equally true for all cultivars used irrespective of their ploidy. Thus, some important features of the (noncanonical) auxin signaling pathways may be variable and species-specific.
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Affiliation(s)
- Sergey N Lomin
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya 35, 127276 Moscow, Russia
| | - Oksana O Kolachevskaya
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya 35, 127276 Moscow, Russia
| | - Dmitry V Arkhipov
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya 35, 127276 Moscow, Russia
| | - Georgy A Romanov
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya 35, 127276 Moscow, Russia
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23
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Grassmann G, Di Rienzo L, Gosti G, Leonetti M, Ruocco G, Miotto M, Milanetti E. Electrostatic complementarity at the interface drives transient protein-protein interactions. Sci Rep 2023; 13:10207. [PMID: 37353566 PMCID: PMC10290103 DOI: 10.1038/s41598-023-37130-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 06/16/2023] [Indexed: 06/25/2023] Open
Abstract
Understanding the mechanisms driving bio-molecules binding and determining the resulting complexes' stability is fundamental for the prediction of binding regions, which is the starting point for drug-ability and design. Characteristics like the preferentially hydrophobic composition of the binding interfaces, the role of van der Waals interactions, and the consequent shape complementarity between the interacting molecular surfaces are well established. However, no consensus has yet been reached on the role of electrostatic. Here, we perform extensive analyses on a large dataset of protein complexes for which both experimental binding affinity and pH data were available. Probing the amino acid composition, the disposition of the charges, and the electrostatic potential they generated on the protein molecular surfaces, we found that (i) although different classes of dimers do not present marked differences in the amino acid composition and charges disposition in the binding region, (ii) homodimers with identical binding region show higher electrostatic compatibility with respect to both homodimers with non-identical binding region and heterodimers. Interestingly, (iii) shape and electrostatic complementarity, for patches defined on short-range interactions, behave oppositely when one stratifies the complexes by their binding affinity: complexes with higher binding affinity present high values of shape complementarity (the role of the Lennard-Jones potential predominates) while electrostatic tends to be randomly distributed. Conversely, complexes with low values of binding affinity exploit Coulombic complementarity to acquire specificity, suggesting that electrostatic complementarity may play a greater role in transient (or less stable) complexes. In light of these results, (iv) we provide a novel, fast, and efficient method, based on the 2D Zernike polynomial formalism, to measure electrostatic complementarity without the need of knowing the complex structure. Expanding the electrostatic potential on a basis of 2D orthogonal polynomials, we can discriminate between transient and permanent protein complexes with an AUC of the ROC of [Formula: see text] 0.8. Ultimately, our work helps shedding light on the non-trivial relationship between the hydrophobic and electrostatic contributions in the binding interfaces, thus favoring the development of new predictive methods for binding affinity characterization.
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Affiliation(s)
- Greta Grassmann
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
- Center for Life Nano & Neuro Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161, Rome, Italy
| | - Lorenzo Di Rienzo
- Center for Life Nano & Neuro Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161, Rome, Italy
| | - Giorgio Gosti
- Center for Life Nano & Neuro Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161, Rome, Italy
- Soft and Living Matter Laboratory, Institute of Nanotechnology, Consiglio Nazionale delle Ricerche, 00185, Rome, Italy
| | - Marco Leonetti
- Center for Life Nano & Neuro Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161, Rome, Italy
- Soft and Living Matter Laboratory, Institute of Nanotechnology, Consiglio Nazionale delle Ricerche, 00185, Rome, Italy
| | - Giancarlo Ruocco
- Center for Life Nano & Neuro Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161, Rome, Italy
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Mattia Miotto
- Center for Life Nano & Neuro Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161, Rome, Italy.
| | - Edoardo Milanetti
- Center for Life Nano & Neuro Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161, Rome, Italy.
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy.
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24
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Li N, Huang X, Shao H. Exploring the pH Sensitivity of Ion-Pair Interactions on a Self-Assembled Monolayer by Scanning Electrochemical Microscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:6529-6538. [PMID: 37116313 DOI: 10.1021/acs.langmuir.3c00469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Insights into the chemical essence of weak interactions on the surface of biomacromolecules may help to regulate biological processes. In this work, the pH sensitivity of ion-pair interactions occurring on a cysteine self-assembled monolayer (Cys SAM) that simulates the local surface of a protein was probed by scanning electrochemical microscopy (SECM). Cys SAM and the ion-pair interactions subsequently formed with the introduced aspartic acid (Asp) were both pH-sensitive, as confirmed by the tip current changes in the feedback mode. After continuous pH measurements, the most significant negative feedback was observed at pH 5.50, indicating the most robust ion-pair interactions, which were simultaneously identified by voltammetry. In this case, the extra addition of the inorganic cation (i.e., Ca2+) did not disrupt the existing ion-pair interactions, and the binding constant (K) and Gibbs free energy (ΔGo) of the ion pair were finally determined to be 6.44 × 105 M-1 and -33.14 kJ mol-1, respectively. Overall, the pH sensitivity of ion-pair interactions was found to be mainly attributable to pH-induced changes in the deprotonated/protonated states of the α-amino acid moieties, which may provide insights into the artificial manipulation of complex binding events at the molecular level on the biological surface.
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Affiliation(s)
- Na Li
- Key Laboratory of Cluster Science (Ministry of Education), Beijing Key Laboratory of Photoelectronic and Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing102488, P. R. China
| | - Ximing Huang
- School of Food and Chemical Engineering, Shaoyang University, Shaoyang 422000, Hunan, P. R. China
| | - Huibo Shao
- Key Laboratory of Cluster Science (Ministry of Education), Beijing Key Laboratory of Photoelectronic and Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing102488, P. R. China
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25
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Fernández-Sánchez SY, Cerón-Carrasco JP, Risco C, Fernández de Castro I. Antiviral Activity of Acetylsalicylic Acid against Bunyamwera Virus in Cell Culture. Viruses 2023; 15:v15040948. [PMID: 37112928 PMCID: PMC10141918 DOI: 10.3390/v15040948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
The Bunyavirales order is a large group of RNA viruses that includes important pathogens for humans, animals and plants. With high-throughput screening of clinically tested compounds we have looked for potential inhibitors of the endonuclease domain of a bunyavirus RNA polymerase. From a list of fifteen top candidates, five compounds were selected and their antiviral properties studied with Bunyamwera virus (BUNV), a prototypic bunyavirus widely used for studies about the biology of this group of viruses and to test antivirals. Four compounds (silibinin A, myricetin, L-phenylalanine and p-aminohippuric acid) showed no antiviral activity in BUNV-infected Vero cells. On the contrary, acetylsalicylic acid (ASA) efficiently inhibited BUNV infection with a half maximal inhibitory concentration (IC50) of 2.02 mM. In cell culture supernatants, ASA reduced viral titer up to three logarithmic units. A significant dose-dependent reduction of the expression levels of Gc and N viral proteins was also measured. Immunofluorescence and confocal microscopy showed that ASA protects the Golgi complex from the characteristic BUNV-induced fragmentation in Vero cells. Electron microscopy showed that ASA inhibits the assembly of Golgi-associated BUNV spherules that are the replication organelles of bunyaviruses. As a consequence, the assembly of new viral particles is also significantly reduced. Considering its availability and low cost, the potential usability of ASA to treat bunyavirus infections deserves further investigation.
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Affiliation(s)
| | - José P Cerón-Carrasco
- Centro Universitario de la Defensa, Universidad Politécnica de Cartagena, C/Coronel López Peña s/n, Base Aérea de San Javier, Santiago de la Ribera, 30720 Murcia, Spain
| | - Cristina Risco
- Cell Structure Laboratory, Centro Nacional de Biotecnología, CSIC, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Isabel Fernández de Castro
- Cell Structure Laboratory, Centro Nacional de Biotecnología, CSIC, Campus de Cantoblanco, 28049 Madrid, Spain
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26
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Gul I, Hassan A, Haq E, Ahmad SM, Shah RA, Ganai NA, Chikan NA, Abdul-Careem MF, Shabir N. An Investigation of the Antiviral Potential of Phytocompounds against Avian Infectious Bronchitis Virus through Template-Based Molecular Docking and Molecular Dynamics Simulation Analysis. Viruses 2023; 15:v15040847. [PMID: 37112828 PMCID: PMC10144825 DOI: 10.3390/v15040847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/17/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Vaccination is widely used to control Infectious Bronchitis in poultry; however, the limited cross-protection and safety issues associated with these vaccines can lead to vaccination failures. Keeping these limitations in mind, the current study explored the antiviral potential of phytocompounds against the Infectious Bronchitis virus using in silico approaches. A total of 1300 phytocompounds derived from fourteen botanicals were screened for their potential ability to inhibit the main protease, papain-like protease or RNA-dependent RNA–polymerase of the virus. The study identified Methyl Rosmarinate, Cianidanol, Royleanone, and 6,7-Dehydroroyleanone as dual-target inhibitors against any two of the key proteins. At the same time, 7-alpha-Acetoxyroyleanone from Rosmarinus officinalis was found to be a multi-target protein inhibitor against all three proteins. The potential multi-target inhibitor was subjected to molecular dynamics simulations to assess the stability of the protein–ligand complexes along with the corresponding reference ligands. The findings specified stable interactions of 7-alpha-Acetoxyroyleanone with the protein targets. The results based on the in silico study indicate that the phytocompounds can potentially inhibit the essential proteins of the Infectious Bronchitis virus; however, in vitro and in vivo studies are required for validation. Nevertheless, this study is a significant step in exploring the use of botanicals in feed to control Infectious Bronchitis infections in poultry.
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Affiliation(s)
- Irfan Gul
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar 190006, India; (I.G.)
- Department of Biotechnology, University of Kashmir, Srinagar 190006, India
| | - Amreena Hassan
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar 190006, India; (I.G.)
- Department of Biotechnology, University of Kashmir, Srinagar 190006, India
| | - Ehtishamul Haq
- Department of Biotechnology, University of Kashmir, Srinagar 190006, India
| | - Syed Mudasir Ahmad
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar 190006, India; (I.G.)
| | - Riaz Ahmad Shah
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar 190006, India; (I.G.)
| | - Nazir Ahmad Ganai
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar 190006, India; (I.G.)
| | - Naveed Anjum Chikan
- Division of Computational Biology, Daskdan Innovations, Pvt. Ltd., Kashmir 190006, India
| | - Mohamed Faizal Abdul-Careem
- Faculty of Veterinary Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
- Correspondence: (M.F.A.-C.); (N.S.)
| | - Nadeem Shabir
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar 190006, India; (I.G.)
- Correspondence: (M.F.A.-C.); (N.S.)
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27
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Paria P, Tassanakajon A. Identification of Potential Druggable Targets and Structure-Based Virtual Screening for Drug-like Molecules against the Shrimp Pathogen Enterocytozoon hepatopenaei. Int J Mol Sci 2023; 24:ijms24021412. [PMID: 36674953 PMCID: PMC9867128 DOI: 10.3390/ijms24021412] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/26/2022] [Accepted: 01/05/2023] [Indexed: 01/13/2023] Open
Abstract
Enterocytozoon hepatopenaei (EHP) causes slow growth syndrome in shrimp, resulting in huge economic losses for the global shrimp industry. Despite worldwide reports, there are no effective therapeutics for controlling EHP infections. In this study, five potential druggable targets of EHP, namely, aquaporin (AQP), cytidine triphosphate (CTP) synthase, thymidine kinase (TK), methionine aminopeptidase2 (MetAP2), and dihydrofolate reductase (DHFR), were identified via functional classification of the whole EHP proteome. The three-dimensional structures of the proteins were constructed using the artificial-intelligence-based program AlphaFold 2. Following the prediction of druggable sites, the ZINC15 and ChEMBL databases were screened against targets using docking-based virtual screening. Molecules with affinity scores ≥ 7.5 and numbers of interactions ≥ 9 were initially selected and subsequently enriched based on their ADMET properties and electrostatic complementarities. Five compounds were finally selected against each target based on their complex stabilities and binding energies. The compounds CHEMBL3703838, CHEMBL2132563, and CHEMBL133039 were selected against AQP; CHEMBL1091856, CHEMBL1162979, and CHEMBL525202 against CTP synthase; CHEMBL4078273, CHEMBL1683320, and CHEMBL3674540 against TK; CHEMBL340488, CHEMBL1966988, and ZINC000828645375 against DHFR; and CHEMBL3913373, ZINC000016682972, and CHEMBL3142997 against MetAP2.The compounds exhibited high stabilities and low binding free energies, indicating their abilities to suppress EHP infections; however, further validation is necessary for determining their efficacy.
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Verma H, Doshi J, Narendra G, Raju B, Singh PK, Silakari O. Energy decomposition and waterswapping analysis to investigate the SNP associated DPD mediated 5-FU resistance. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2023; 34:39-64. [PMID: 36779961 DOI: 10.1080/1062936x.2023.2165146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 12/31/2022] [Indexed: 06/18/2023]
Abstract
5-fluorouracil is an essential component of systemic chemotherapy for colon, breast, head, and neck cancer patients. However, tumoral overexpression of the dihydropyrimidine dehydrogenase has rendered 5-FU clinically ineffective by inactivating it to 5'-6'-dihydro fluorouracil. The responses to 5-FU in terms of efficacy and toxicity greatly differ depending upon the population group, because of variability in the DPD activity levels. In the current study, key active site amino acids involved in the 5-FU inactivation were investigated by modelling the 3D structure of human DPD in a complex with 5-FU. The identified amino acids were analyzed for their possible missense mutations available in dbSNP database. Out of 12 missense SNPs, four were validated either by sequencing in the 1000 Genomes project or frequency/genotype data. The recorded validated missense SNPs were further considered to analyze the effect of their respective alterations on 5-FU binding. Overall findings suggested that population bearing the Glu611Val DPD mutation (rs762523739) is highly vulnerable to 5-FU resistance. From the docking, electrostatic complementarity, dynamics, and energy decomposition analyses it was found that the above mutation showed superior scores than the wild DPD -5FU complex. Therefore, prescribing prodrug NUC-3373 or DPD inhibitors (Gimeracil/3-Cyano-2,6-Dihydroxypyridines) as adjuvant therapy may overcome the 5-FU resistance.
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Affiliation(s)
- H Verma
- Molecular Modelling Laboratory (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, India
| | - J Doshi
- BioInsight Solutions, Mumbai, India
| | - G Narendra
- Molecular Modelling Laboratory (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, India
| | - B Raju
- Molecular Modelling Laboratory (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, India
| | - P K Singh
- Integrative Physiology and Pharmacology, Institute of Biomedicine, Faculty of Medicine, University of Turku, Turku, Finland
| | - O Silakari
- Molecular Modelling Laboratory (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, India
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Roja R, Kalakotla S, Ravula AR, Boyina HK, Navanita SK, Vallika PBS, Gangarapu K, Devarakonda KP, Bakshi V. Insilico Screening of Pentacyclic Triterpenoids against Vascular Dementia Target's. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1423:237-243. [PMID: 37525050 DOI: 10.1007/978-3-031-31978-5_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Vascular dementia (VaD) accounts to 30% of cases and is predicted as second most common form of dementia after Alzheimer's disease by WHO. Earlier studies reported that plant-derived pentacyclic triterpenoids possess a wide range of pharmacological activities but these compounds are not extensively studied for their neuroprotective potential against VaD. This in silico approach was designed to screen 20 pentacyclic triterpenoid plant compounds against known targets of VaD using Flare software. S-Adenyl homocysteine hydrolase, Acetylcholinesterase, and Butyrylcholinesterase were selected as important VaD targets, and various parameters like intermolecular interaction energies, binding energy, and dock scores were analyzed and compared between selected ligands. Our results showed that Ursolic acid has lowest binding energy when docked with most of the target proteins, and among all 20 pentacyclic triterpenoids studied, only three ligands Betulinic acid, Ambolic acid, and Madecassic acid, showed better binding energy scores, and they can be shortlisted as lead compounds to further study their therapeutic potential against VaD using in vitro and in vivo animal models.
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Affiliation(s)
- Rathna Roja
- School of Pharmacy, Department of Pharmacology, Anurag University, Hyderabad, Telangana, India
| | - Shanker Kalakotla
- Department of Pharmacognosy & Phyto-Pharmacy, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Nilgiris, Tamil Nadu, India
| | - Arun Reddy Ravula
- Department of Biomedical Engineering, Center for Injury Biomechanics, Materials and Medicine, New Jersey Institute of Technology, Newark, NJ, USA
| | - Hemanth Kumar Boyina
- School of Pharmacy, Department of Pharmacology, Anurag University, Hyderabad, Telangana, India
| | - S K Navanita
- Department of Pharmacognosy & Phyto-Pharmacy, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Nilgiris, Tamil Nadu, India
| | | | - Kiran Gangarapu
- School of Pharmacy, Department of Pharmaceutical Analysis, Anurag University, Hyderabad, Telangana, India
| | | | - Vasudha Bakshi
- School of Pharmacy, Department of Pharmacology, Anurag University, Hyderabad, Telangana, India
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30
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Andole S, Sd H, Sudhula S, Vislavath L, Boyina HK, Gangarapu K, Bakshi V, Devarakonda KP. 3D QSAR based Virtual Screening of Flavonoids as Acetylcholinesterase Inhibitors. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1424:233-240. [PMID: 37486499 DOI: 10.1007/978-3-031-31982-2_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
In an attempt to develop therapeutic agents to treat Alzheimer's disease, a series of flavonoid analogues were collected, which already had established acetylcholinesterase (AChE) enzyme inhibition activity. For each molecule we also collected biological activity data (Ki). Then, 3D-QSAR (quantitative structure-activity relationship model) was developed which showed acceptable predictive and descriptive capability as represented by standard statistical parameters r2 and q2. This SAR data can explain the key descriptors which can be related to AChE inhibitory activity. Using the QSAR model, pharmacophores were developed based on which, virtual screening was done and a dataset was obtained which loaded as a prediction set to fit the developed QSAR model. Top 10 compounds fitting the QSAR model were subjected to molecular docking. CHEMBL1718051 was found to be the lead compound. This study is offering an example of a computationally-driven tool for prioritisation and discovery of probable AChE inhibitors. Further, in vivo and in vitro testing will show its therapeutic potential.
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Affiliation(s)
- Sowmya Andole
- School of Pharmacy, Department of Pharmacology, Anurag University, Hyderabad, Telangana, India
| | - Husna Sd
- School of Pharmacy, Department of Pharmacology, Anurag University, Hyderabad, Telangana, India
| | - Srija Sudhula
- School of Pharmacy, Department of Pharmacology, Anurag University, Hyderabad, Telangana, India
| | - Lavanya Vislavath
- School of Pharmacy, Department of Pharmacology, Anurag University, Hyderabad, Telangana, India
| | - Hemanth Kumar Boyina
- School of Pharmacy, Department of Pharmacology, Anurag University, Hyderabad, Telangana, India
| | - Kiran Gangarapu
- School of Pharmacy, Department of Pharmaceutical Analysis, Anurag University, Hyderabad, Telangana, India
| | - Vasudha Bakshi
- School of Pharmacy, Department of Pharmacology, Anurag University, Hyderabad, Telangana, India
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31
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Alshammari MM, Soury R, Alenezi KM, Mushtque M, Rizvi MMA, Haque A. Synthesis, characterization, anticancer and in silico studies of a pyrazole-tethered thiazolidine-2,4-dione derivative. J Biomol Struct Dyn 2022; 40:13075-13082. [PMID: 34551668 DOI: 10.1080/07391102.2021.1981451] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A new pyrazole-tethered thiazolidine-2,4-dione derivative (8) has been synthesized by the Knoevenagel condensation of 3-(4-nitrophenyl)-1-phenyl-1H-pyrazole-4-carbaldehyde (4) and 3-(2,4-dioxothiazolidin-3-yl)propanenitrile (7). The structure of the final compound was confirmed by standard spectroscopic techniques including IR spectroscopy, 1H-NMR spectroscopy, and ESI-MS mass spectrometry. Molecular features including frontier molecular orbital (HOMO-LUMO) energies, reactivity descriptors and molecular electrostatic potential (ESP) of the title molecule were determined using density functional theory (DFT) calculation. The in vitro cytotoxicity of both the intermediate (4) and final (8) compounds were investigated against cancerous (SW-480 and MCF-7) and normal (HEK-293) cell lines by MTT assay. Compound (8) displayed higher activity than (4) with higher sensitivity against breast cancer cell line and lesser toxicity. The experimental data were further complemented by docking and absorption, distribution, metabolism, and excretion (ADME) studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Musherah M Alshammari
- Department of Chemistry, College of Science, University of Hail, Ha'il, Kingdom of Saudi Arabia
| | - Raoudha Soury
- Department of Chemistry, College of Science, University of Hail, Ha'il, Kingdom of Saudi Arabia
| | - Khalaf M Alenezi
- Department of Chemistry, College of Science, University of Hail, Ha'il, Kingdom of Saudi Arabia
| | - Md Mushtque
- School of Physical and Molecular Sciences, Department of Chemistry, Al-Falah University, Dhauj, Faridabad, Haryana, India
| | | | - Ashanul Haque
- Department of Chemistry, College of Science, University of Hail, Ha'il, Kingdom of Saudi Arabia
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32
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Elinson MN, Vereshchagin AN, Ryzhkova YE, Karpenko KA, Ryzhkov FV, Egorov MP. Electrocatalytic Cascade Selective Approach to 3-Aryl-2' H,3 H,4 H-Spiro{Furo[2,3- с]Chromene-2,5'-Pyrimidine}-2',4,4',6'(1' H,3' H)Tetraones and Its Automatic Screening Docking Studies. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2149568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Affiliation(s)
- Michail N. Elinson
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Anatoly N. Vereshchagin
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Yuliya E. Ryzhkova
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Kirill A. Karpenko
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Fedor V. Ryzhkov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Mikhail P. Egorov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
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33
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Rushworth J, Thawani AR, Fajardo-Ruiz E, Meiring JCM, Heise C, White AJP, Akhmanova A, Brandt JR, Thorn-Seshold O, Fuchter MJ. [5]-Helistatins: Tubulin-Binding Helicenes with Antimitotic Activity. JACS AU 2022; 2:2561-2570. [PMID: 36465552 PMCID: PMC9709948 DOI: 10.1021/jacsau.2c00435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/06/2022] [Accepted: 10/06/2022] [Indexed: 06/17/2023]
Abstract
Helicenes are high interest synthetic targets with unique conjugated helical structures that have found important technological applications. Despite this interest, helicenes have had limited impact in chemical biology. Herein, we disclose a first-in-class antimitotic helicene, helistatin 1 (HA-1), where the helicene scaffold acts as a structural mimic of colchicine, a known antimitotic drug. The synthesis proceeds via sequential Pd-catalyzed coupling reactions and a π-Lewis acid cycloisomerization mediated by PtCl2. HA-1 was found to block microtubule polymerization in both cell-free and live cell assays. Not only does this demonstrate the feasibility of using helicenes as bioactive scaffolds against protein targets, but also suggests wider potential for the use of helicenes as isosteres of biaryls or cis-stilbenes-themselves common drug and natural product scaffolds. Overall, this study further supports future opportunities for helicenes for a range of chemical biological applications.
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Affiliation(s)
- James
L. Rushworth
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, 82 Wood Lane, London W12 OBZ, U.K.
| | - Aditya R. Thawani
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, 82 Wood Lane, London W12 OBZ, U.K.
| | - Elena Fajardo-Ruiz
- Department
of Pharmacy, Ludwig-Maximilians University
of Munich, Munich 81377, Germany
| | - Joyce C. M. Meiring
- Cell
Biology, Neurobiology and Biophysics, Department of Biology, Faculty
of Science, Utrecht University, Utrecht 3584 CH, Netherlands
| | - Constanze Heise
- Department
of Pharmacy, Ludwig-Maximilians University
of Munich, Munich 81377, Germany
| | - Andrew J. P. White
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, 82 Wood Lane, London W12 OBZ, U.K.
| | - Anna Akhmanova
- Cell
Biology, Neurobiology and Biophysics, Department of Biology, Faculty
of Science, Utrecht University, Utrecht 3584 CH, Netherlands
| | - Jochen R. Brandt
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, 82 Wood Lane, London W12 OBZ, U.K.
| | - Oliver Thorn-Seshold
- Department
of Pharmacy, Ludwig-Maximilians University
of Munich, Munich 81377, Germany
| | - Matthew J. Fuchter
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, 82 Wood Lane, London W12 OBZ, U.K.
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Ryzhkova YE, Elinson MN, Vereshchagin AN, Kalashnikova VM, Korolev VA, Ryzhkov FV, Egorov MP. Green electrocatalytic Assembling of Salicylaldehydes, Kojic Acid, and Malonic Acid Derivatives into 2‐amino‐4H‐chromenes as Potent Anti‐inflammatory Agents. ChemistrySelect 2022. [DOI: 10.1002/slct.202202872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yuliya E. Ryzhkova
- N. D. Zelinsky Institute of Organic Chemistry Russian academy of sciences, Leninsky pr. 47 Moscow 119991 Russian Federation
| | - Michail N. Elinson
- N. D. Zelinsky Institute of Organic Chemistry Russian academy of sciences, Leninsky pr. 47 Moscow 119991 Russian Federation
| | - Anatoly N. Vereshchagin
- N. D. Zelinsky Institute of Organic Chemistry Russian academy of sciences, Leninsky pr. 47 Moscow 119991 Russian Federation
| | - Varvara M. Kalashnikova
- N. D. Zelinsky Institute of Organic Chemistry Russian academy of sciences, Leninsky pr. 47 Moscow 119991 Russian Federation
- D. I. Mendeleev University of Chemical Technology of Russia Miusskaya sq. 9 Moscow 125047 Russian Federation
| | - Victor A. Korolev
- N. D. Zelinsky Institute of Organic Chemistry Russian academy of sciences, Leninsky pr. 47 Moscow 119991 Russian Federation
| | - Fedor V. Ryzhkov
- N. D. Zelinsky Institute of Organic Chemistry Russian academy of sciences, Leninsky pr. 47 Moscow 119991 Russian Federation
| | - Mikhail P. Egorov
- N. D. Zelinsky Institute of Organic Chemistry Russian academy of sciences, Leninsky pr. 47 Moscow 119991 Russian Federation
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35
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Jackson V, Jordan L, Burgin RN, McGaw OJS, Muir CW, Ceban V. Application of Molecular-Modeling, Scaffold-Hopping, and Bioisosteric Approaches to the Discovery of New Heterocyclic Picolinamides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:11031-11041. [PMID: 35852973 DOI: 10.1021/acs.jafc.2c03755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Macrocyclic natural products and their derivatives are a valuable source for biologically active crop protection products and have had significant impact on the development of conventional agrochemicals. However, they can be challenging starting points for lead-generation efforts because of their size, structural complexity, and developability. Using molecular modeling and electrostatic analysis, alternative bicyclic isosteres were identified as replacements for the antifungal nine-membered macrocycle UK-2A. By application of a structure-based conformational approach, a series of heterocyclic replacements were derivatized to deliver promising fungicidal activity and scaffold bioisosteres were further diversified to investigate structure-activity relationships.
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Affiliation(s)
- Victoria Jackson
- Globachem Discovery, Mereside, Alderley Park, Macclesfield SK10 4TG, United Kingdom
| | - Linda Jordan
- Globachem Discovery, Mereside, Alderley Park, Macclesfield SK10 4TG, United Kingdom
| | - Ryan N Burgin
- Globachem Discovery, Mereside, Alderley Park, Macclesfield SK10 4TG, United Kingdom
| | - Oliver J S McGaw
- Globachem Discovery, Mereside, Alderley Park, Macclesfield SK10 4TG, United Kingdom
| | - Calum W Muir
- Globachem Discovery, Mereside, Alderley Park, Macclesfield SK10 4TG, United Kingdom
| | - Victor Ceban
- Globachem Discovery, Mereside, Alderley Park, Macclesfield SK10 4TG, United Kingdom
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36
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Raju B, Narendra G, Verma H, Kumar M, Sapra B, Kaur G, jain SK, Silakari O. Machine Learning Enabled Structure-Based Drug Repurposing Approach to Identify Potential CYP1B1 Inhibitors. ACS OMEGA 2022; 7:31999-32013. [PMID: 36120033 PMCID: PMC9476183 DOI: 10.1021/acsomega.2c02983] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Drug-metabolizing enzyme (DME)-mediated pharmacokinetic resistance of some clinically approved anticancer agents is one of the main reasons for cancer treatment failure. In particular, some commonly used anticancer medicines, including docetaxel, tamoxifen, imatinib, cisplatin, and paclitaxel, are inactivated by CYP1B1. Currently, no approved drugs are available to treat this CYP1B1-mediated inactivation, making the pharmaceutical industries strive to discover new anticancer agents. Because of the extreme complexity and high risk in drug discovery and development, it is worthwhile to come up with a drug repurposing strategy that may solve the resistance problem of existing chemotherapeutics. Therefore, in the current study, a drug repurposing strategy was implemented to find the possible CYP1B1 inhibitors using machine learning (ML) and structure-based virtual screening (SB-VS) approaches. Initially, three different ML models were developed such as support vector machines (SVMs), random forest (RF), and artificial neural network (ANN); subsequently, the best-selected ML model was employed for virtual screening of the selleckchem database to identify potential CYP1B1 inhibitors. The inhibition potency of the obtained hits was judged by analyzing the crucial active site amino acid interactions against CYP1B1. After a thorough assessment of docking scores, binding affinities, as well as binding modes, four compounds were selected and further subjected to in vitro analysis. From the in vitro analysis, it was observed that chlorprothixene, nadifloxacin, and ticagrelor showed promising inhibitory activity toward CYP1B1 in the IC50 range of 0.07-3.00 μM. These new chemical scaffolds can be explored as adjuvant therapies to address CYP1B1-mediated drug-resistance problems.
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Affiliation(s)
- Baddipadige Raju
- Molecular
Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug
Research, Punjabi University, Patiala, Punjab 147002, India
| | - Gera Narendra
- Molecular
Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug
Research, Punjabi University, Patiala, Punjab 147002, India
| | - Himanshu Verma
- Molecular
Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug
Research, Punjabi University, Patiala, Punjab 147002, India
| | - Manoj Kumar
- Molecular
Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug
Research, Punjabi University, Patiala, Punjab 147002, India
| | - Bharti Sapra
- Molecular
Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug
Research, Punjabi University, Patiala, Punjab 147002, India
| | - Gurleen Kaur
- Center
for Basic and Translational Research in Health Sciences, Guru Nanak Dev University, Amritsar 143005, India
| | - Subheet Kumar jain
- Center
for Basic and Translational Research in Health Sciences, Guru Nanak Dev University, Amritsar 143005, India
| | - Om Silakari
- Molecular
Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug
Research, Punjabi University, Patiala, Punjab 147002, India
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37
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Singh M, Verma H, Bhandu P, Kumar M, Narendra G, Choudhary S, Singh PK, Silakari O. Network Analysis Guided Designing of Multi-Targeted Anti-Fungal Agents: Synthesis and Biological Evaluation. J Mol Struct 2022; 1272:134128. [PMID: 36101882 PMCID: PMC9458262 DOI: 10.1016/j.molstruc.2022.134128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/20/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022]
Abstract
During the ongoing pandemic, there have been increasing reports of invasive fungal disease (IFD), particularly among immunocompromised populations. Candida albicans is one of the most common clinical pathogenic microorganisms which have become a serious health threat to population either infected with Covid-19 or on treatment with immunosuppressant's/broad-range antibiotics. Currently, benzothiazole is a well explored scaffold for anti-fungal activity, especially mercapto substituted benzothiazoles. It is reported that exploring the 2nd position of benzothiazoles yield improved anti-fungal molecules. Therefore, in the current study, lead optimization approach using bioisosteric replacement protocol was followed to improve the anti-fungal activity of an already reported benzothiazole derivative, N-(1,3-benzothiazole-2-yl)-2-(pyridine-3-ylformohydrazido) acetamide. To rationally identify the putative anti-candida targets of this derivative, network analysis was carried out. Complexes of designed compounds and identified putative targets were further analyzed for the docking interactions and their consequent retention after the completion of exhaustive MD simulations. Top seven designed compounds were synthesized and evaluated for in-vitro anti-fungal property against Candida, which indicated that compounds 1.2c and 1.2f possess improved and comparable anti-fungal activity to N-(1,3-benzothiazole-2-yl)-2-(pyridine-3-ylformohydrazido) acetamide and Nystatin, respectively.
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Affiliation(s)
- Manmeet Singh
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, India
| | - Himanshu Verma
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, India
| | - Priyanka Bhandu
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, India
| | - Manoj Kumar
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, India
| | - Gera Narendra
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, India
| | - Shalki Choudhary
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, India
| | - Pankaj Kumar Singh
- Faculty of Medicine, Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, Turku, FI-20014, Finland
| | - Om Silakari
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, India
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38
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Zhao L, Pu M, Wang H, Ma X, Zhang YJ. Modified Electrostatic Complementary Score Function and Its Application Boundary Exploration in Drug Design. J Chem Inf Model 2022; 62:4420-4426. [PMID: 36069259 DOI: 10.1021/acs.jcim.2c00616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In recent years, machine learning (ML) models have been found to quickly predict various molecular properties with accuracy comparable to high-level quantum chemistry methods. One such example is the calculation of electrostatic potential (ESP). Different ESP prediction ML models were proposed to generate surface molecular charge distribution. Electrostatic complementarity (EC) can apply ESP data to quantify the complementarity between a ligand and its binding pocket, leading to the potential to increase the efficiency of drug design. However, there is not much research discussing EC score functions and their applicability domain. We propose a new EC score function modified from the one originally developed by Bauer and Mackey, and confirm its effectiveness against the available Pearson's R correlation coefficient. Additionally, the applicability domain of the EC score and two indices used to define the EC score application scope will be discussed.
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Affiliation(s)
- Liming Zhao
- Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China
| | - Mengchen Pu
- Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China
| | - Huting Wang
- Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China
| | - Xiangyu Ma
- Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China
| | - Yingsheng J Zhang
- Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China
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New Imaging Modality of COVID-19 Pneumonia Developed on the Basis of Alzheimer’s Disease Research. Int J Mol Sci 2022; 23:ijms23158405. [PMID: 35955536 PMCID: PMC9369300 DOI: 10.3390/ijms23158405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/20/2022] [Accepted: 07/27/2022] [Indexed: 11/30/2022] Open
Abstract
Viral pneumonia caused by highly infectious SARS-CoV-2 poses a higher risk to older people and those who have underlying health conditions, including Alzheimer’s disease. In this work we present newly designed tacrine-based radioconjugates with physicochemical and biological properties that are crucial for the potential application as diagnostic radiopharmaceuticals. A set of ten tacrine derivatives was synthesized, labelled with gallium-68 and fully characterized in the context of their physicochemical properties. Based on these results, the final two most promising radioconjugates, [68Ga]Ga-NODAGA-Bn-NH(CH2)9Tac and [68Ga]Ga-THP-NH(CH2)9Tac, were selected for biodistribution studies. The latter compound was proven to be a good inhibitor of cholinesterases with significant affinity toward the lungs, according to the biodistribution studies. On the basis of molecular modelling combined with in vitro studies, we unraveled which structural properties of the developed tacrine derivatives are crucial for high affinity toward acetylcholinesterase, whose increased levels in lung tissues in the course of coronavirus disease indicate the onset of pneumonia. The radiopharmaceutical [68Ga]Ga-THP-NH(CH2)9Tac was ultimately selected due to its increased accuracy and improved sensitivity in PET imaging of lung tissue with high levels of acetylcholinesterase, and it may become a novel potential diagnostic modality for the determination of lung perfusion, including in inflammation after COVID-19.
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Walters RK, Gale EM, Barnoud J, Glowacki DR, Mulholland AJ. The emerging potential of interactive virtual reality in drug discovery. Expert Opin Drug Discov 2022; 17:685-698. [PMID: 35638298 DOI: 10.1080/17460441.2022.2079632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
INTRODUCTION The potential of virtual reality (VR) to contribute to drug design and development has been recognized for many years. A recent advance is to use VR not only to visualize and interact with molecules, but also to interact with molecular dynamics simulations 'on the fly' (interactive molecular dynamics in VR, IMD-VR), which is useful for flexible docking and examining binding processes and conformational changes. AREAS COVERED The authors use the term 'interactive VR' to refer to software where interactivity is an inherent part of the user VR experience e.g. in making structural modifications or interacting with a physically rigorous molecular dynamics (MD) simulation, as opposed to using VR controllers to rotate and translate the molecule for enhanced visualization. Here, they describe these methods and their application to problems relevant to drug discovery, highlighting the possibilities that they offer in this arena. EXPERT OPINION The ease of viewing and manipulating molecular structures and dynamics, using accessible VR hardware, and the ability to modify structures on the fly (e.g. adding or deleting atoms) - and for groups of researchers to work together in the same virtual environment - makes modern interactive VR a valuable tool to add to the armory of drug design and development methods.
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Affiliation(s)
- Rebecca K Walters
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | - Ella M Gale
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | - Jonathan Barnoud
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
- CiTIUS Intelligent Technologies Research Centre, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - David R Glowacki
- CiTIUS Intelligent Technologies Research Centre, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
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Studies on the antiviral activity of chebulinic acid against dengue and chikungunya viruses and in silico investigation of its mechanism of inhibition. Sci Rep 2022; 12:10397. [PMID: 35729191 PMCID: PMC9213501 DOI: 10.1038/s41598-022-13923-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 05/30/2022] [Indexed: 11/08/2022] Open
Abstract
Chebulinic acid (CA), originally isolated from the flower extract of the plant Terminalia chebula, has been shown to inhibit infection of herpes simplex virus-2 (HSV-2), suggestively by inhibiting the host entry step of viral infection. Like HSV-2, the dengue virus (DENV) and chikungunya virus (CHIKV) also use receptor glycosaminoglycans (GAG) to gain host entry, therefore, the activity of CA was tested against these viruses. Co-treatment of 8 µM CA with DENV-2 caused 2 log decrease in the virus titer (4.0 log10FFU/mL) at 120 h post infection, compared to virus control (5.95 log10FFU/mL). In contrast, no inhibitory effect of CA was observed against CHIKV infection under any condition. The mechanism of action of CA was investigated in silico by employing DENV-2 and CHIKV envelope glycoproteins. During docking, CA demonstrated equivalent binding at multiple sites on DENV-2 envelope protein, including GAG binding site, which have previously been reported to play a crucial role in host attachment and fusion, indicating blocking of these sites. However, CA did not show binding to the GAG binding site on envelope protein-2 of CHIKV. The in vitro and in silico findings suggest that CA possesses the ability to inhibit DENV-2 infection at the entry stage of its infection cycle and may be developed as a potential therapeutic agent against it.
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Multicomponent Electrocatalytic Selective Approach to Unsymmetrical Spiro[furo[3,2-c]pyran-2,5′-pyrimidine] Scaffold under a Column Chromatography-Free Protocol at Room Temperature. CHEMISTRY 2022. [DOI: 10.3390/chemistry4020044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Electrochemical synthesis suggested a mild, green and atom-efficient route to interesting and useful molecules, thus avoiding harsh chemical oxidizing and reducing agents used in traditional synthetic methods. Organic electrochemistry offers an excellent alternative to conventional methods of organic synthesis and creates a modern tool for carrying out organic synthesis, including cascade and multicomponent ones. In this research, a novel electrocatalytic multicomponent transformation was found: the electrochemical multicomponent assembly of arylaldehydes, N,N′-dimethylbarbituric acid and 4-hydroxy-6-methyl-2H-pyran-2-one in one pot reaction was carried out in alcohols in an undivided cell in the presence of alkali metal halides with the selective formation of substituted unsymmetrical 1′,3′,6-trimethyl-3-aryl-2′H,3H,4H-spiro[furo[3,2-c]pyran-2,5′-pyrimidine]-2′,4,4′,6′(1′H,3′H)-tetraones in 73–82% yields. This new electrocatalytic process is a selective, facile and efficient way to obtain spiro[furo[3,2-c]pyran-2,5′-pyrimidines]. According to screening molecular docking data using a self-made Python script in Flare, all synthesized compounds may be prominent for different medical applications, such as breast cancer, neurodegenerative diseases and treatments connected with urinary tract, bones and the cardiovascular system.
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Nguyen M, An S, Nguyen Y, Hyun YE, Choi H, Pham L, Kim JA, Noh M, Kim G, Jeong LS. Design, Synthesis, and Biological Activity of l-1′-Homologated Adenosine Derivatives. ACS Med Chem Lett 2022; 13:1131-1136. [DOI: 10.1021/acsmedchemlett.2c00159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Mai Nguyen
- College of Pharmacy and Research Institute of Drug Development, Chonnam National University, Gwangju 61186, Korea
| | - Seungchan An
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea
- Natural Products Research Institute, Seoul National University, Seoul 08826, Korea
| | - Yen Nguyen
- College of Pharmacy and Research Institute of Drug Development, Chonnam National University, Gwangju 61186, Korea
| | - Young Eum Hyun
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Hongseok Choi
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Linh Pham
- College of Pharmacy and Research Institute of Drug Development, Chonnam National University, Gwangju 61186, Korea
| | - Jung-Ae Kim
- College of Pharmacy, Yeungnam University, Gyeongsan 38541, Korea
| | - Minsoo Noh
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea
- Natural Products Research Institute, Seoul National University, Seoul 08826, Korea
| | - Gyudong Kim
- College of Pharmacy and Research Institute of Drug Development, Chonnam National University, Gwangju 61186, Korea
| | - Lak Shin Jeong
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea
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Gan HH, Zinno J, Piano F, Gunsalus KC. Omicron Spike Protein Has a Positive Electrostatic Surface That Promotes ACE2 Recognition and Antibody Escape. FRONTIERS IN VIROLOGY 2022. [DOI: 10.3389/fviro.2022.894531] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
High transmissibility is a hallmark of the Omicron variant of SARS-CoV-2. Understanding the molecular determinants of Omicron’s transmissibility will impact development of intervention strategies. Here we map the electrostatic potential surface of the Spike protein to show that major SARS-CoV-2 variants have accumulated positive charges in solvent-exposed regions of the Spike protein, especially its ACE2-binding interface. Significantly, the Omicron Spike-ACE2 complex has complementary electrostatic surfaces. In contrast, interfaces between Omicron and neutralizing antibodies tend to have similar positively charged surfaces. Structural modeling demonstrates that the electrostatic property of Omicron’s Spike receptor binding domain (S RBD) plays a role in enhancing ACE2 recognition and destabilizing Spike-antibody complexes. Specifically, the Omicron S RBD has favorable electrostatic interaction energy with ACE2 that is 3-5 times greater than the Delta variant over a range of 20 Å, implying efficient recognition of host receptors. Computed binding affinities of six representative S RBD-antibody complexes show that Omicron can escape most antibodies targeting the ACE2-binding region of S RBD. Interestingly, a straightforward assessment of the electrostatic surfaces of 18 neutralizing antibodies correctly predicted the Omicron escape status of 80% of cases. Collectively, our structural analysis implies that Omicron S RBD interaction interfaces have been optimized to simultaneously promote access to human ACE2 receptors and evade antibodies. These findings suggest that electrostatic interactions are a major contributing factor for increased Omicron transmissibility relative to other variants.
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Cox PB, Gupta R. Contemporary Computational Applications and Tools in Drug Discovery. ACS Med Chem Lett 2022; 13:1016-1029. [DOI: 10.1021/acsmedchemlett.1c00662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Philip B. Cox
- Drug Discovery Science and Technology, AbbVie, 1 North Waukegan Road, North Chicago, Illinois 60064-6217, United States
| | - Rishi Gupta
- Drug Discovery Science and Technology, AbbVie, 1 North Waukegan Road, North Chicago, Illinois 60064-6217, United States
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Verma H, Narendra G, Raju B, Kumar M, Jain SK, Tung GK, Singh PK, Silakari O. 3D-QSAR and scaffold hopping based designing of benzo[d]ox-azol-2(3H)-one and 2-oxazolo[4,5-b]pyridin-2(3H)-one derivatives as selective aldehyde dehydrogenase 1A1 inhibitors: Synthesis and biological evaluation. Arch Pharm (Weinheim) 2022; 355:e2200108. [PMID: 35618489 DOI: 10.1002/ardp.202200108] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/26/2022] [Accepted: 05/02/2022] [Indexed: 01/16/2023]
Abstract
Aldehyde dehydrogenase 1 (ALDH1A1), an oxidoreductase class of enzymes, is overexpressed in various types of cancer cell lines and is the major cause of resistance to the Food and Drug Administration (FDA)-approved drug, cyclophosphamide (CP). In cancer conditions, CP undergoes a sequence of biotransformations to form an active metabolite, aldophosphamide, which further biotransforms to its putative cytotoxic metabolite, phosphoramide mustard. However, in resistant cancer conditions, aldophosphamide is converted into its inactive metabolite, carboxyphosphamide, via oxidation with ALDH1A1. Herein, to address the issue of ALDH1A1 mediated CP resistance, we report a series of benzo[d]oxazol-2(3H)-one and 2-oxazolo[4,5-b]pyridin-2(3H)-one derivatives as selective ALDH1A1 inhibitors. These inhibitors were designed using a validated 3D-quantitative structure activity relationship (3D-QSAR) model coupled with scaffold hopping. The 3D-QSAR model was developed using reported indole-2,3-diones based ALDH1A1 inhibitors, which provided field points in terms of electrostatic, van der Waals and hydrophobic potentials required for selectively inhibiting ALDH1A1. The most selective indole-2,3-diones-based compound, that is, cmp 3, was further considered for scaffold hopping. Two top-ranked bioisosteres, that is, benzo[d]oxazol-2(3H)-one and 2-oxazolo[4,5-b]pyridin-2(3H)-one, were selected for designing new inhibitors by considering the field pattern of 3D-QSAR. All designed molecules were mapped perfectly on the 3D-QSAR model and found to be predictive with good inhibitory potency (pIC50 range: 7.5-6.8). Molecular docking was carried out for each designed molecule to identify key interactions that are required for ALDH1A1 inhibition and to authenticate the 3D-QSAR result. The top five inhibitor-ALDH1A1 complexes were also submitted for molecular dynamics simulations to access their stability. In vitro enzyme assays of 21 compounds suggested that these compounds are selective toward ALDH1A1 over the other two isoforms, that is, ALDH2 and ALDH3A1. All the compounds were found to be at least three and two times more selective toward ALDH1A1 over ALDH2 and ALDH3A1, respectively. All the compounds showed an IC50 value in the range of 0.02-0.80 μM, which indicates the potential for these to be developed as adjuvant therapy for CP resistance.
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Affiliation(s)
- Himanshu Verma
- Molecular Modelling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, India
| | - Gera Narendra
- Molecular Modelling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, India
| | - Baddipadige Raju
- Molecular Modelling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, India
| | - Manoj Kumar
- Molecular Modelling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, India
| | - Subheet K Jain
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, India
| | - Gurleen K Tung
- Centre for Basic and Translational Research in Health Sciences, Guru Nanak Dev University, Amritsar, India
| | - Pankaj K Singh
- Faculty of Medicine, Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Om Silakari
- Molecular Modelling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, India
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Novel Cyclopentaquinoline and Acridine Analogs as Multifunctional, Potent Drug Candidates in Alzheimer's Disease. Int J Mol Sci 2022; 23:ijms23115876. [PMID: 35682556 PMCID: PMC9179981 DOI: 10.3390/ijms23115876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 02/06/2023] Open
Abstract
A series of new cyclopentaquinoline derivatives with 9-acridinecarboxylic acid and a different alkyl chain length were synthesized, and their ability to inhibit cholinesterases was evaluated. All designed compounds, except derivative 3f, exhibited a selectivity for butyrylcholinesterase (BuChE) with IC50 values ranging from 103 to 539 nM. The 3b derivative revealed the highest inhibitory activity towards BuChE (IC50 = 103.73 nM) and a suitable activity against AChE (IC50 = 272.33 nM). The 3f derivative was the most active compound to AChE (IC50 = 113.34 nM) with satisfactory activity towards BuChE (IC50 = 203.52 nM). The potential hepatotoxic effect was evaluated for both 3b and 3f compounds. The 3b and 3f potential antioxidant activity was measured using the ORAC-FL method. The 3b and 3f derivatives revealed a significantly higher antioxidant potency, respectively 35 and 25 higher than tacrine. Theoretical, physicochemical, and pharmacokinetic properties were calculated using ACD Labs Percepta software. Molecular modeling and kinetic study were used to reveal the mechanism of cholinesterase inhibition in the most potent compounds: 3b and 3f.
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Islas ÁA, Scior T. Allosteric Binding of MDMA to the Human Serotonin Transporter (hSERT) via Ensemble Binding Space Analysis with ΔG Calculations, Induced Fit Docking and Monte Carlo Simulations. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27092977. [PMID: 35566327 PMCID: PMC9099856 DOI: 10.3390/molecules27092977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 11/16/2022]
Abstract
Despite the recent promising results of MDMA (3,4-methylenedioxy-methamphetamine) as a psychotherapeutic agent and its history of misuse, little is known about its molecular mode of action. MDMA enhances monoaminergic neurotransmission in the brain and its valuable psychoactive effects are associated to a dual action on the 5-HT transporter (SERT). This drug inhibits the reuptake of 5-HT (serotonin) and reverses its flow, acting as a substrate for the SERT, which possesses a central binding site (S1) for antidepressants as well as an allosteric (S2) one. Previously, we characterized the spatial binding requirements for MDMA at S1. Here, we propose a structure-based mechanistic model of MDMA occupation and translocation across both binding sites, applying ensemble binding space analyses, electrostatic complementarity, and Monte Carlo energy perturbation theory. Computed results were correlated with experimental data (r = 0.93 and 0.86 for S1 and S2, respectively). Simulations on all hSERT available structures with Gibbs free energy estimations (ΔG) revealed a favourable and pervasive dual binding mode for MDMA at S2, i.e., adopting either a 5-HT or an escitalopram-like orientation. Intermediate ligand conformations were identified within the allosteric site and between the two sites, outlining an internalization pathway for MDMA. Among the strongest and more frequent interactions were salt bridges with Glu494 and Asp328, a H-bond with Thr497, a π-π with Phe556, and a cation-π with Arg104. Similitudes and differences with the allosteric binding of 5-HT and antidepressants suggest that MDMA may have a distinctive chemotype. Thus, our models may provide a framework for future virtual screening studies and pharmaceutical design and to develop hSERT allosteric compounds with a unique psychoactive MDMA-like profile.
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Affiliation(s)
- Ángel A. Islas
- Vicerrectoría de Investigación y Estudios de Posgrado, Benemérita Universidad Autónoma de Puebla, Puebla 72592, Mexico
- Laboratory of Computational Molecular Simulations, Departamento de Farmacia, Benemérita Universidad Autónoma de Puebla, Puebla 72592, Mexico;
- Correspondence:
| | - Thomas Scior
- Laboratory of Computational Molecular Simulations, Departamento de Farmacia, Benemérita Universidad Autónoma de Puebla, Puebla 72592, Mexico;
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Cons BD, Twigg DG, Kumar R, Chessari G. Electrostatic Complementarity in Structure-Based Drug Design. J Med Chem 2022; 65:7476-7488. [PMID: 35512344 DOI: 10.1021/acs.jmedchem.2c00164] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Optimization of electrostatic complementarity is an important strategy in structure-based drug discovery for improving the affinity of molecules against a specific protein target. In this Miniperspective we identify examples where deliberate optimization of protein-ligand electrostatic complementarity or intramolecular electrostatic interactions gave improvements in target affinity (up to 250-fold), physicochemical properties, in vitro properties, and off-target selectivity. We also look retrospectively at a series of factor Xa inhibitors that show an almost 8000-fold range in potency that can be correlated with the calculated electrostatic potential (ESP) surfaces. Recent developments using a graph-convolutional deep neural network to rapidly generate high quality ESP surfaces have the potential to make this useful tool more accessible for a wider audience within the field of medicinal chemistry.
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Affiliation(s)
- Benjamin D Cons
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - David G Twigg
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Rajendra Kumar
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Gianni Chessari
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
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50
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Liu J, Zhou T, Li R, Tian Z. Structural insights into the discrepant synergistic activity of Codlemone and (Z)-8-dodecenol towards Grapholita molesta pheromones. PEST MANAGEMENT SCIENCE 2022; 78:1953-1962. [PMID: 35085422 DOI: 10.1002/ps.6813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/20/2021] [Accepted: 01/22/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Insect pheromone synergists have been widely used to produce potent pheromone products for environment-friendly pest control. Codlemone (Cod) and (Z)-8-dodecenol (Dod) are two major Grapholita molesta pheromone synergists, with Cod having greater synergism and affinity for G. molesta pheromone binding protein 2 (GmolPBP2). Uncovering structural information key to the different binding affinity of Cod and Dod to GmolPBP2 would gain insights into what causes their synergy activity discrepancy. RESULTS Binding modes of the two synergists in the binding pocket of GmolPBP2 were analyzed and compared by molecular dynamics-based approaches. Although Cod and Dod were stabilized in a similar hydrophobic pocket, their interaction details with GmolPBP2 were divergent due to the extra double bond (C10═C11) in Cod. The C10═C11 improved the hydrophobic interactions of Cod with around residues. Such hydrophobic interaction improvement was also reflected in the raised importance of Phe11 in the GmolPBP2-Cod interaction. Not only that, the increased hydrophobic forces introduced by the C10═C11 changed the CH2-OH orientation in the GmolPBP2-Cod complex, which improved the H-bond interaction. Electrostatic complementarity analysis further indicated the positive role of C10═C11 in optimizing GmolPBP2-Cod interaction. CONCLUSION The C10═C11 is thought to contribute greatly to Cod's stronger synergy as a group key to the higher GmolPBP2-affinity, based on which the improvement directions for Cod and Dod were addressed as well. Our findings will aid in the development and optimization of more effective pheromone synergists, resulting in more effective pheromone-based pest management.
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Affiliation(s)
- Jiyuan Liu
- Key Laboratory of Plant Protection Resources & Pest Management of the Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Tong Zhou
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Ruichi Li
- Key Laboratory of Plant Protection Resources & Pest Management of the Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Zhen Tian
- Key Laboratory of Plant Protection Resources & Pest Management of the Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, China
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
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