Loading…
Steered Molecular Dynamics Simulations Study on FABP4 Inhibitors
Ordinary small molecule de novo drug design is time-consuming and expensive. Recently, computational tools were employed and proved their efficacy in accelerating the overall drug design process. Molecular dynamics (MD) simulations and a derivative of MD, steered molecular dynamics (SMD), turned out...
Saved in:
| Published in: | Molecules (Basel, Switzerland) Switzerland), 2023-03, Vol.28 (6), p.2731 |
|---|---|
| Main Authors: | , , , , , , |
| Format: | Article |
| Language: | English |
| Subjects: | |
| Citations: | Items that this one cites Items that cite this one |
| Online Access: | Get full text |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| cited_by | cdi_FETCH-LOGICAL-c561t-4cf196778eaa80b99a0a8b517ab46f6496deec46e171dabc1fb486e5d9f3f7553 |
|---|---|
| cites | cdi_FETCH-LOGICAL-c561t-4cf196778eaa80b99a0a8b517ab46f6496deec46e171dabc1fb486e5d9f3f7553 |
| container_end_page | |
| container_issue | 6 |
| container_start_page | 2731 |
| container_title | Molecules (Basel, Switzerland) |
| container_volume | 28 |
| creator | Tomarchio, Rosario Patamia, Vincenzo Zagni, Chiara Crocetti, Letizia Cilibrizzi, Agostino Floresta, Giuseppe Rescifina, Antonio |
| description | Ordinary small molecule de novo drug design is time-consuming and expensive. Recently, computational tools were employed and proved their efficacy in accelerating the overall drug design process. Molecular dynamics (MD) simulations and a derivative of MD, steered molecular dynamics (SMD), turned out to be promising rational drug design tools. In this paper, we report the first application of SMD to evaluate the binding properties of small molecules toward FABP4, considering our recent interest in inhibiting fatty acid binding protein 4 (FABP4). FABP4 inhibitors (FABP4is) are small molecules of therapeutic interest, and ongoing clinical studies indicate that they are promising for treating cancer and other diseases such as metabolic syndrome and diabetes. |
| doi_str_mv | 10.3390/molecules28062731 |
| format | article |
| fullrecord | <record><control><sourceid>gale_doaj_</sourceid><recordid>TN_cdi_doaj_primary_oai_doaj_org_article_2b0a43a1625447a1a4e92baa91a01624</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A743768681</galeid><doaj_id>oai_doaj_org_article_2b0a43a1625447a1a4e92baa91a01624</doaj_id><sourcerecordid>A743768681</sourcerecordid><originalsourceid>FETCH-LOGICAL-c561t-4cf196778eaa80b99a0a8b517ab46f6496deec46e171dabc1fb486e5d9f3f7553</originalsourceid><addsrcrecordid>eNptkktv1DAUhSMEoqXwA9igSGzYTPH7sYKhUBipCKTC2rpxbqYeJXFrJ0jz7_EwpXQAeWHr-JzPute3qp5Tcsq5Ja-H2KOfe8zMEMU0pw-qYyoYWXAi7MN756PqSc4bQhgVVD6ujriyRmpCj6u3lxNiwrb-vGdBqt9vRxiCz_VlGIowhTiW8zS32zqO9fny3VdRr8ar0IQppvy0etRBn_HZ7X5SfT__8O3s0-Liy8fV2fJi4aWi00L4jlqltUEAQxprgYBpJNXQCNUpYVWL6IVCqmkLjaddI4xC2dqOd1pKflKt9tw2wsZdpzBA2roIwf0SYlo7SFPwPTrWEBAcqGJSCA0UBFrWAFgKpIiisN7sWddzM2DrcZwS9AfQw5sxXLl1_OEoIdJwpgrh1S0hxZsZ8-SGkD32PYwY5-yYtkwSwygr1pd_WTdxTmPp1c5FlZHS2j-uNZQKwtjF8rDfQd1SC66VUYYW1-l_XGW1WH4sjtiFoh8E6D7gU8w5YXdXJCVuN0PunxkqmRf3u3OX-D00_CeBhcIh</addsrcrecordid><sourcetype>Open Website</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2791685599</pqid></control><display><type>article</type><title>Steered Molecular Dynamics Simulations Study on FABP4 Inhibitors</title><source>Publicly Available Content (ProQuest)</source><source>PubMed Central</source><source>Coronavirus Research Database</source><creator>Tomarchio, Rosario ; Patamia, Vincenzo ; Zagni, Chiara ; Crocetti, Letizia ; Cilibrizzi, Agostino ; Floresta, Giuseppe ; Rescifina, Antonio</creator><creatorcontrib>Tomarchio, Rosario ; Patamia, Vincenzo ; Zagni, Chiara ; Crocetti, Letizia ; Cilibrizzi, Agostino ; Floresta, Giuseppe ; Rescifina, Antonio</creatorcontrib><description>Ordinary small molecule de novo drug design is time-consuming and expensive. Recently, computational tools were employed and proved their efficacy in accelerating the overall drug design process. Molecular dynamics (MD) simulations and a derivative of MD, steered molecular dynamics (SMD), turned out to be promising rational drug design tools. In this paper, we report the first application of SMD to evaluate the binding properties of small molecules toward FABP4, considering our recent interest in inhibiting fatty acid binding protein 4 (FABP4). FABP4 inhibitors (FABP4is) are small molecules of therapeutic interest, and ongoing clinical studies indicate that they are promising for treating cancer and other diseases such as metabolic syndrome and diabetes.</description><identifier>ISSN: 1420-3049</identifier><identifier>EISSN: 1420-3049</identifier><identifier>DOI: 10.3390/molecules28062731</identifier><identifier>PMID: 36985701</identifier><language>eng</language><publisher>Switzerland: MDPI AG</publisher><subject>Atherosclerosis ; Binding sites ; Colorectal cancer ; Computer applications ; computer-aided drug design ; Design ; Diabetes mellitus ; Drug Design ; Drug development ; FABP4 ; FABP4 inhibitors ; Fatty acid-binding protein ; Fatty Acid-Binding Proteins - metabolism ; Fatty acids ; Health aspects ; Humans ; Inhibitors ; Ligands ; Medical research ; Medicine, Experimental ; Metabolic disorders ; Metabolic Syndrome ; Metastasis ; Molecular dynamics ; Molecular Dynamics Simulation ; molecular modeling ; Monte Carlo simulation ; Protein binding ; Proteins ; R&D ; Research & development ; Simulation methods ; Software ; steered molecular dynamics</subject><ispartof>Molecules (Basel, Switzerland), 2023-03, Vol.28 (6), p.2731</ispartof><rights>COPYRIGHT 2023 MDPI AG</rights><rights>2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2023 by the authors. 2023</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c561t-4cf196778eaa80b99a0a8b517ab46f6496deec46e171dabc1fb486e5d9f3f7553</citedby><cites>FETCH-LOGICAL-c561t-4cf196778eaa80b99a0a8b517ab46f6496deec46e171dabc1fb486e5d9f3f7553</cites><orcidid>0000-0002-9711-5183 ; 0000-0002-0668-1260 ; 0000-0003-3473-2683 ; 0000-0001-5039-2151 ; 0000-0002-0048-2631 ; 0000-0003-1220-4281</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.proquest.com/docview/2791685599/fulltextPDF?pq-origsite=primo$$EPDF$$P50$$Gproquest$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/2791685599?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,25731,27901,27902,36989,36990,38493,43871,44566,53766,53768,74155,74869</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/36985701$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Tomarchio, Rosario</creatorcontrib><creatorcontrib>Patamia, Vincenzo</creatorcontrib><creatorcontrib>Zagni, Chiara</creatorcontrib><creatorcontrib>Crocetti, Letizia</creatorcontrib><creatorcontrib>Cilibrizzi, Agostino</creatorcontrib><creatorcontrib>Floresta, Giuseppe</creatorcontrib><creatorcontrib>Rescifina, Antonio</creatorcontrib><title>Steered Molecular Dynamics Simulations Study on FABP4 Inhibitors</title><title>Molecules (Basel, Switzerland)</title><addtitle>Molecules</addtitle><description>Ordinary small molecule de novo drug design is time-consuming and expensive. Recently, computational tools were employed and proved their efficacy in accelerating the overall drug design process. Molecular dynamics (MD) simulations and a derivative of MD, steered molecular dynamics (SMD), turned out to be promising rational drug design tools. In this paper, we report the first application of SMD to evaluate the binding properties of small molecules toward FABP4, considering our recent interest in inhibiting fatty acid binding protein 4 (FABP4). FABP4 inhibitors (FABP4is) are small molecules of therapeutic interest, and ongoing clinical studies indicate that they are promising for treating cancer and other diseases such as metabolic syndrome and diabetes.</description><subject>Atherosclerosis</subject><subject>Binding sites</subject><subject>Colorectal cancer</subject><subject>Computer applications</subject><subject>computer-aided drug design</subject><subject>Design</subject><subject>Diabetes mellitus</subject><subject>Drug Design</subject><subject>Drug development</subject><subject>FABP4</subject><subject>FABP4 inhibitors</subject><subject>Fatty acid-binding protein</subject><subject>Fatty Acid-Binding Proteins - metabolism</subject><subject>Fatty acids</subject><subject>Health aspects</subject><subject>Humans</subject><subject>Inhibitors</subject><subject>Ligands</subject><subject>Medical research</subject><subject>Medicine, Experimental</subject><subject>Metabolic disorders</subject><subject>Metabolic Syndrome</subject><subject>Metastasis</subject><subject>Molecular dynamics</subject><subject>Molecular Dynamics Simulation</subject><subject>molecular modeling</subject><subject>Monte Carlo simulation</subject><subject>Protein binding</subject><subject>Proteins</subject><subject>R&D</subject><subject>Research & development</subject><subject>Simulation methods</subject><subject>Software</subject><subject>steered molecular dynamics</subject><issn>1420-3049</issn><issn>1420-3049</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><sourceid>COVID</sourceid><sourceid>PIMPY</sourceid><sourceid>DOA</sourceid><recordid>eNptkktv1DAUhSMEoqXwA9igSGzYTPH7sYKhUBipCKTC2rpxbqYeJXFrJ0jz7_EwpXQAeWHr-JzPute3qp5Tcsq5Ja-H2KOfe8zMEMU0pw-qYyoYWXAi7MN756PqSc4bQhgVVD6ujriyRmpCj6u3lxNiwrb-vGdBqt9vRxiCz_VlGIowhTiW8zS32zqO9fny3VdRr8ar0IQppvy0etRBn_HZ7X5SfT__8O3s0-Liy8fV2fJi4aWi00L4jlqltUEAQxprgYBpJNXQCNUpYVWL6IVCqmkLjaddI4xC2dqOd1pKflKt9tw2wsZdpzBA2roIwf0SYlo7SFPwPTrWEBAcqGJSCA0UBFrWAFgKpIiisN7sWddzM2DrcZwS9AfQw5sxXLl1_OEoIdJwpgrh1S0hxZsZ8-SGkD32PYwY5-yYtkwSwygr1pd_WTdxTmPp1c5FlZHS2j-uNZQKwtjF8rDfQd1SC66VUYYW1-l_XGW1WH4sjtiFoh8E6D7gU8w5YXdXJCVuN0PunxkqmRf3u3OX-D00_CeBhcIh</recordid><startdate>20230301</startdate><enddate>20230301</enddate><creator>Tomarchio, Rosario</creator><creator>Patamia, Vincenzo</creator><creator>Zagni, Chiara</creator><creator>Crocetti, Letizia</creator><creator>Cilibrizzi, Agostino</creator><creator>Floresta, Giuseppe</creator><creator>Rescifina, Antonio</creator><general>MDPI AG</general><general>MDPI</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BENPR</scope><scope>CCPQU</scope><scope>COVID</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>K9.</scope><scope>M0S</scope><scope>M1P</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0002-9711-5183</orcidid><orcidid>https://orcid.org/0000-0002-0668-1260</orcidid><orcidid>https://orcid.org/0000-0003-3473-2683</orcidid><orcidid>https://orcid.org/0000-0001-5039-2151</orcidid><orcidid>https://orcid.org/0000-0002-0048-2631</orcidid><orcidid>https://orcid.org/0000-0003-1220-4281</orcidid></search><sort><creationdate>20230301</creationdate><title>Steered Molecular Dynamics Simulations Study on FABP4 Inhibitors</title><author>Tomarchio, Rosario ; Patamia, Vincenzo ; Zagni, Chiara ; Crocetti, Letizia ; Cilibrizzi, Agostino ; Floresta, Giuseppe ; Rescifina, Antonio</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c561t-4cf196778eaa80b99a0a8b517ab46f6496deec46e171dabc1fb486e5d9f3f7553</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Atherosclerosis</topic><topic>Binding sites</topic><topic>Colorectal cancer</topic><topic>Computer applications</topic><topic>computer-aided drug design</topic><topic>Design</topic><topic>Diabetes mellitus</topic><topic>Drug Design</topic><topic>Drug development</topic><topic>FABP4</topic><topic>FABP4 inhibitors</topic><topic>Fatty acid-binding protein</topic><topic>Fatty Acid-Binding Proteins - metabolism</topic><topic>Fatty acids</topic><topic>Health aspects</topic><topic>Humans</topic><topic>Inhibitors</topic><topic>Ligands</topic><topic>Medical research</topic><topic>Medicine, Experimental</topic><topic>Metabolic disorders</topic><topic>Metabolic Syndrome</topic><topic>Metastasis</topic><topic>Molecular dynamics</topic><topic>Molecular Dynamics Simulation</topic><topic>molecular modeling</topic><topic>Monte Carlo simulation</topic><topic>Protein binding</topic><topic>Proteins</topic><topic>R&D</topic><topic>Research & development</topic><topic>Simulation methods</topic><topic>Software</topic><topic>steered molecular dynamics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Tomarchio, Rosario</creatorcontrib><creatorcontrib>Patamia, Vincenzo</creatorcontrib><creatorcontrib>Zagni, Chiara</creatorcontrib><creatorcontrib>Crocetti, Letizia</creatorcontrib><creatorcontrib>Cilibrizzi, Agostino</creatorcontrib><creatorcontrib>Floresta, Giuseppe</creatorcontrib><creatorcontrib>Rescifina, Antonio</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>ProQuest Central</collection><collection>ProQuest One Community College</collection><collection>Coronavirus Research Database</collection><collection>ProQuest Central</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Publicly Available Content (ProQuest)</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>Directory of Open Access Journals</collection><jtitle>Molecules (Basel, Switzerland)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Tomarchio, Rosario</au><au>Patamia, Vincenzo</au><au>Zagni, Chiara</au><au>Crocetti, Letizia</au><au>Cilibrizzi, Agostino</au><au>Floresta, Giuseppe</au><au>Rescifina, Antonio</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Steered Molecular Dynamics Simulations Study on FABP4 Inhibitors</atitle><jtitle>Molecules (Basel, Switzerland)</jtitle><addtitle>Molecules</addtitle><date>2023-03-01</date><risdate>2023</risdate><volume>28</volume><issue>6</issue><spage>2731</spage><pages>2731-</pages><issn>1420-3049</issn><eissn>1420-3049</eissn><abstract>Ordinary small molecule de novo drug design is time-consuming and expensive. Recently, computational tools were employed and proved their efficacy in accelerating the overall drug design process. Molecular dynamics (MD) simulations and a derivative of MD, steered molecular dynamics (SMD), turned out to be promising rational drug design tools. In this paper, we report the first application of SMD to evaluate the binding properties of small molecules toward FABP4, considering our recent interest in inhibiting fatty acid binding protein 4 (FABP4). FABP4 inhibitors (FABP4is) are small molecules of therapeutic interest, and ongoing clinical studies indicate that they are promising for treating cancer and other diseases such as metabolic syndrome and diabetes.</abstract><cop>Switzerland</cop><pub>MDPI AG</pub><pmid>36985701</pmid><doi>10.3390/molecules28062731</doi><orcidid>https://orcid.org/0000-0002-9711-5183</orcidid><orcidid>https://orcid.org/0000-0002-0668-1260</orcidid><orcidid>https://orcid.org/0000-0003-3473-2683</orcidid><orcidid>https://orcid.org/0000-0001-5039-2151</orcidid><orcidid>https://orcid.org/0000-0002-0048-2631</orcidid><orcidid>https://orcid.org/0000-0003-1220-4281</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1420-3049 |
| ispartof | Molecules (Basel, Switzerland), 2023-03, Vol.28 (6), p.2731 |
| issn | 1420-3049 1420-3049 |
| language | eng |
| recordid | cdi_doaj_primary_oai_doaj_org_article_2b0a43a1625447a1a4e92baa91a01624 |
| source | Publicly Available Content (ProQuest); PubMed Central; Coronavirus Research Database |
| subjects | Atherosclerosis Binding sites Colorectal cancer Computer applications computer-aided drug design Design Diabetes mellitus Drug Design Drug development FABP4 FABP4 inhibitors Fatty acid-binding protein Fatty Acid-Binding Proteins - metabolism Fatty acids Health aspects Humans Inhibitors Ligands Medical research Medicine, Experimental Metabolic disorders Metabolic Syndrome Metastasis Molecular dynamics Molecular Dynamics Simulation molecular modeling Monte Carlo simulation Protein binding Proteins R&D Research & development Simulation methods Software steered molecular dynamics |
| title | Steered Molecular Dynamics Simulations Study on FABP4 Inhibitors |
| url | http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-05T23%3A46%3A30IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_doaj_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Steered%20Molecular%20Dynamics%20Simulations%20Study%20on%20FABP4%20Inhibitors&rft.jtitle=Molecules%20(Basel,%20Switzerland)&rft.au=Tomarchio,%20Rosario&rft.date=2023-03-01&rft.volume=28&rft.issue=6&rft.spage=2731&rft.pages=2731-&rft.issn=1420-3049&rft.eissn=1420-3049&rft_id=info:doi/10.3390/molecules28062731&rft_dat=%3Cgale_doaj_%3EA743768681%3C/gale_doaj_%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c561t-4cf196778eaa80b99a0a8b517ab46f6496deec46e171dabc1fb486e5d9f3f7553%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=2791685599&rft_id=info:pmid/36985701&rft_galeid=A743768681&rfr_iscdi=true |