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Wei M, Chen J, Song Y, Monserrat JP, Zhang Y, Shen L. Progress on synthesis and structure-activity relationships of lamellarins over the past decade. Eur J Med Chem 2024; 269:116294. [PMID: 38508119 DOI: 10.1016/j.ejmech.2024.116294] [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: 12/25/2023] [Revised: 02/28/2024] [Accepted: 02/28/2024] [Indexed: 03/22/2024]
Abstract
Lamellarins are polyaromatic alkaloids isolated from marine organisms, including mollusks, tunicates, and sponges. Currently, over 60 structurally distinct natural lamellarins have been reported, and most of them exhibit promising biological activities, such as topoisomerase inhibition, mitochondrial function inhibition, multidrug resistance reversing, and anti-HIV activity. There has also been a significant progress on the synthetic study of lamellarins which has been regularly updated by numerous medicinal chemists as well. This review provides a detailed summary of the synthesis, pharmacology, and structural modification of lamellarins over the past decades.
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Affiliation(s)
- Mingze Wei
- School of Pharmaceutical Science, Zhejiang Chinese Medical University, 310061, Hangzhou, China
| | - Jing Chen
- School of Pharmaceutical Science, Zhejiang Chinese Medical University, 310061, Hangzhou, China
| | - Yuliang Song
- School of Pharmaceutical Science, Zhejiang Chinese Medical University, 310061, Hangzhou, China
| | | | - Yongmin Zhang
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire, UMR 8232, 4 place Jussieu, 75005 Paris, France
| | - Li Shen
- School of Pharmaceutical Science, Zhejiang Chinese Medical University, 310061, Hangzhou, China.
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Two Decades of 4D-QSAR: A Dying Art or Staging a Comeback? Int J Mol Sci 2021; 22:ijms22105212. [PMID: 34069090 PMCID: PMC8156896 DOI: 10.3390/ijms22105212] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 01/01/2023] Open
Abstract
A key question confronting computational chemists concerns the preferable ligand geometry that fits complementarily into the receptor pocket. Typically, the postulated ‘bioactive’ 3D ligand conformation is constructed as a ‘sophisticated guess’ (unnecessarily geometry-optimized) mirroring the pharmacophore hypothesis—sometimes based on an erroneous prerequisite. Hence, 4D-QSAR scheme and its ‘dialects’ have been practically implemented as higher level of model abstraction that allows the examination of the multiple molecular conformation, orientation and protonation representation, respectively. Nearly a quarter of a century has passed since the eminent work of Hopfinger appeared on the stage; therefore the natural question occurs whether 4D-QSAR approach is still appealing to the scientific community? With no intention to be comprehensive, a review of the current state of art in the field of receptor-independent (RI) and receptor-dependent (RD) 4D-QSAR methodology is provided with a brief examination of the ‘mainstream’ algorithms. In fact, a myriad of 4D-QSAR methods have been implemented and applied practically for a diverse range of molecules. It seems that, 4D-QSAR approach has been experiencing a promising renaissance of interests that might be fuelled by the rising power of the graphics processing unit (GPU) clusters applied to full-atom MD-based simulations of the protein-ligand complexes.
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Alp Tokat T, Türkmenoğlu B, Güzel Y, Kızılcan DŞ. Investigation of 3D pharmacophore of N-benzyl benzamide molecules of melanogenesis inhibitors using a new descriptor Klopman index: uncertainties in model. J Mol Model 2019; 25:247. [PMID: 31342175 DOI: 10.1007/s00894-019-4120-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 07/03/2019] [Indexed: 12/21/2022]
Abstract
We used a new descriptor called the Klopman index in our software of the "molecular comparative electron topology" (MCET) method to reduce the uncertainty resulting from the descriptors used in QSAR studies. The 3D pharmacophore model (3D-PhaM), which can demonstrate three-dimensional interaction between the ligand -receptor (L-R), is only possible with local reactive descriptors (LRD). The Klopman index, containing both Coulombic and frontier orbital and interactions of atoms of the ligand, is a good LRD. Molecular conformers having the best matching atoms with the template conformer can be selected as one of the most suitable spatial structures for interaction with the receptor, and the LRD values of the atoms in this conformer serve to determine 3D-PhaM. The 3D-PhaM of the N-benzyl benzamide derivatives, such as the melanogenesis inhibitor, was determined by ligand-based MCET and confirmed by the structure-based FlexX docking method. For compounds of the training set (42) and the external cross validation test set (6), the Q2 (0.862) and R2 (0.913) of the statistical parameters were calculated, respectively, and were checked by rm2 (0.85) of the stringent validation.
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Affiliation(s)
- Tuğba Alp Tokat
- Department of Chemistry, Faculty of Science, Erciyes University, 38039, Kayseri, Turkey
| | - Burçin Türkmenoğlu
- Department of Chemistry, Faculty of Science, Erciyes University, 38039, Kayseri, Turkey.
| | - Yahya Güzel
- Department of Chemistry, Faculty of Science, Erciyes University, 38039, Kayseri, Turkey
| | - Dilek Şeyma Kızılcan
- Department of Chemistry, Faculty of Science, Erciyes University, 38039, Kayseri, Turkey
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Dittrich N, Pilkington LI, Leung E, Barker D. Synthesis of N -benzyl-des- D -ring lamellarin K via an acyl-Claisen/Paal-Knorr approach. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.02.044] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Bak A, Kozik V, Smolinski A, Jampilek J. Multidimensional (3D/4D-QSAR) probability-guided pharmacophore mapping: investigation of activity profile for a series of drug absorption promoters. RSC Adv 2016. [DOI: 10.1039/c6ra15820j] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A hybrid approach that combines 3D and 4D-QSAR methods based on grid and neural paradigms with automated IVE-PLS procedure was examined to identify the pharmacophore pattern for cholic acid derivatives as potential drug absorption promoters.
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Affiliation(s)
- A. Bak
- Department of Organic Chemistry
- Institute of Chemistry
- University of Silesia
- Katowice
- Poland
| | - V. Kozik
- Department of Synthesis Chemistry
- Institute of Chemistry
- University of Silesia
- Katowice
- Poland
| | - A. Smolinski
- Department of Energy Saving and Air Protection
- Central Mining Institute
- Katowice
- Poland
| | - J. Jampilek
- Department of Pharmaceutical Chemistry
- Faculty of Pharmacy
- Comenius University
- Bratislava
- Slovakia
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Shi MW, Sobolev AN, Schirmeister T, Engels B, Schmidt TC, Luger P, Mebs S, Dittrich B, Chen YS, Bąk JM, Jayatilaka D, Bond CS, Turner MJ, Stewart SG, Spackman MA, Grabowsky S. Electrostatic complementarity in pseudoreceptor modeling based on drug molecule crystal structures: the case of loxistatin acid (E64c). NEW J CHEM 2015. [DOI: 10.1039/c4nj01503g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A combination of pseudoreceptor modeling and electrostatic complementarity maps properties of a native pocket for an enzyme ligand.
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Quantitative structure–activity relationship (QSAR) studies as strategic approach in drug discovery. Med Chem Res 2014. [DOI: 10.1007/s00044-014-1072-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Cananzi S, Merlini L, Artali R, Beretta GL, Zaffaroni N, Dallavalle S. Synthesis and topoisomerase I inhibitory activity of a novel diazaindeno[2,1-b]phenanthrene analogue of Lamellarin D. Bioorg Med Chem 2011; 19:4971-84. [PMID: 21783369 DOI: 10.1016/j.bmc.2011.06.056] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 06/16/2011] [Accepted: 06/20/2011] [Indexed: 12/14/2022]
Abstract
A novel 5-oxa-6a,8-diazaindeno[2,1-b]phenanthren-7-one scaffold was designed and synthesized as an active analogue of the cytotoxic marine alkaloid Lamellarin D. The design was based on molecular modeling of the site of interaction of Lamellarin D with DNA-topoisomerase I cleavable complex, whereas the synthesis capitalized on a simple Friedel-Crafts cyclization of indole to a β-carbolinone nucleus. The product exhibited topoisomerase I poisoning activity and submicromolar cytotoxicity on human non-small cell lung cancer H460 cell line.
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Affiliation(s)
- Salvatore Cananzi
- Department of Molecular and Agrifood Sciences, Università di Milano, Via Celoria 2, 20133 Milano, Italy
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Development of quantitative structure–activity relationships for explanatory modeling of fast reacting (meth)acrylate monomers bearing novel functionality. J Mol Graph Model 2011; 29:763-72. [DOI: 10.1016/j.jmgm.2010.12.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Accepted: 12/23/2010] [Indexed: 11/21/2022]
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Abstract
The latest developments towards the synthesis of lamellarins, their structure–activity relationship and advances in the mechanism of action are described.
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Affiliation(s)
- Daniel Pla
- CIBER-BBN
- Networking Centre on Bioengineering
- Biomaterials and Nanomedicine
- Barcelona Science Park
- Barcelona
| | - Fernando Albericio
- CIBER-BBN
- Networking Centre on Bioengineering
- Biomaterials and Nanomedicine
- Barcelona Science Park
- Barcelona
| | - Mercedes Álvarez
- CIBER-BBN
- Networking Centre on Bioengineering
- Biomaterials and Nanomedicine
- Barcelona Science Park
- Barcelona
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Exploring the molecular basis for selective cytotoxicity of lamellarins against human hormone-dependent T47D and hormone-independent MDA-MB-231 breast cancer cells. MONATSHEFTE FUR CHEMIE 2010. [DOI: 10.1007/s00706-010-0409-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Andrade CH, Pasqualoto KFM, Ferreira EI, Hopfinger AJ. 4D-QSAR: perspectives in drug design. Molecules 2010; 15:3281-94. [PMID: 20657478 PMCID: PMC6263259 DOI: 10.3390/molecules15053281] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 03/30/2010] [Accepted: 04/06/2010] [Indexed: 12/05/2022] Open
Abstract
Drug design is a process driven by innovation and technological breakthroughs involving a combination of advanced experimental and computational methods. A broad variety of medicinal chemistry approaches can be used for the identification of hits, generation of leads, as well as to accelerate the optimization of leads into drug candidates. The quantitative structure–activity relationship (QSAR) formalisms are among the most important strategies that can be applied for the successful design new molecules. This review provides a comprehensive review on the evolution and current status of 4D-QSAR, highlighting present challenges and new opportunities in drug design.
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Affiliation(s)
- Carolina H. Andrade
- Laboratory of Molecular Modeling, Faculty of Pharmacy, Federal University of Goiás, 1ª Av. c/ Praça Universitária, S/N., Goiânia, Goiás, 74605-220, Brazil
- College of Pharmacy, MSC09 5360, 1 University of New Mexico, Albuquerque, New Mexico 87131-0001, USA; E-Mail: (A.J.H.)
- Author to whom correspondence should be addressed; E-Mail:
| | - Kerly F. M. Pasqualoto
- Faculty of Pharmaceutical Sciences, Av. Prof. Lineu Prestes, 580, University of Sao Paulo, Sao Paulo, 05508-900, Brazil; E-Mails: (K.F.M.P.); (E.I.F.)
| | - Elizabeth I. Ferreira
- Faculty of Pharmaceutical Sciences, Av. Prof. Lineu Prestes, 580, University of Sao Paulo, Sao Paulo, 05508-900, Brazil; E-Mails: (K.F.M.P.); (E.I.F.)
| | - Anton J. Hopfinger
- College of Pharmacy, MSC09 5360, 1 University of New Mexico, Albuquerque, New Mexico 87131-0001, USA; E-Mail: (A.J.H.)
- The Chem21 Group, Inc., 17870 Wilson Drive. Lake Forest, IL 60045, USA
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Thipnate P, Liu J, Hannongbua S, Hopfinger AJ. 3D pharmacophore mapping using 4D QSAR analysis for the cytotoxicity of lamellarins against human hormone-dependent T47D breast cancer cells. J Chem Inf Model 2009; 49:2312-22. [PMID: 19799437 PMCID: PMC2798151 DOI: 10.1021/ci9002427] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
4D quantitative structure-activity relationship (QSAR) and 3D pharmacophore models were built and investigated for cytotoxicity using a training set of 25 lamellarins against human hormone dependent T47D breast cancer cells. Receptor-independent (RI) 4D QSAR models were first constructed from the exploration of eight possible receptor-binding alignments for the entire training set. Since the training set is small (25 compounds), the generality of the 4D QSAR paradigm was then exploited to devise a strategy to maximize the extraction of binding information from the training set and to also permit virtual screening of diverse lamellarin chemistry. 4D QSAR models were sought for only six of the most potent lamellarins of the training set as well as another subset composed of lamellarins with constrained ranges in molecular weight and lipophilicity. This overall modeling strategy has permitted maximizing 3D pharmacophore information from this small set of structurally complex lamellarins that can be used to drive future analog synthesis and the selection of alternate scaffolds. Overall, it was found that the formation of an intermolecular hydrogen bond and the hydrophobic interactions for substituents on the E ring most modulate the cytotoxicity against T47D breast cancer cells. Hydrophobic substitutions on the F-ring can also enhance cytotoxic potency. A complementary high-throughput virtual screen to the 3D pharmacophore models, a 4D fingerprint QSAR model, was constructed using absolute molecular similarity. This 4D fingerprint virtual high-throughput screen permits a larger range of chemistry diversity to be assayed than with the 4D QSAR models. The optimized 4D QSAR 3D pharmacophore model has a leave-one-out cross-correlation value of xv-r2 = 0.947, while the optimized 4D fingerprint virtual screening model has a value of xv-r2 = 0.719. This work reveals that it is possible to develop significant QSAR, 3D pharmacophore, and virtual screening models for a small set of lamellarins showing cytotoxic behavior in breast cancer screens that can guide future drug development based upon lamellarin chemistry.
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Affiliation(s)
- Poonsiri Thipnate
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
- Center of Nanotechnology KU, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Jianzhong Liu
- College of Pharmacy, MSC09 5360, 1 University of New Mexico, Albuquerque, New Mexico 87131-000, USA
- The Chem21 Group, Incorporated, 1780 Wilson Drive, Lake Forest, IL 60045
| | - Supa Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
- Center of Nanotechnology KU, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - A. J. Hopfinger
- College of Pharmacy, MSC09 5360, 1 University of New Mexico, Albuquerque, New Mexico 87131-000, USA
- The Chem21 Group, Incorporated, 1780 Wilson Drive, Lake Forest, IL 60045
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