1
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Yamauchi K, Soyano M, Kobayashi M, Kamatari YO, Mitsunaga T. Protein aggregation model to explain the bioactivity of condensed tannins. Food Chem 2023; 416:135870. [PMID: 36898342 DOI: 10.1016/j.foodchem.2023.135870] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023]
Abstract
Tannins are involved in the taste of foods and multi bioactivity of traditional herbal medicines. The characteristics of tannins are believed to derive from their connectivity with proteins. However, the mode of interaction between proteins and tannins is not yet understood because of the complexity of the tannin structure. Then this study aimed to elucidate the detail binding mode of tannin and protein by the 1H-15N HSQC NMR method using the 15N-labeled MMP-1that have not been used so far. The HSQC results suggested cross-link sites between MMP-1s, which cause protein aggregation and inhibit MMP-1 activity. This study presents the first 3D protein aggregation model of condensed tannins, which is important for understanding the bioactivity of polyphenols. Furthermore, it can broaden the understanding of the range of interactions between other proteins and polyphenols.
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Affiliation(s)
- Kosei Yamauchi
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Gifu 501-1193, Japan.
| | - Mayu Soyano
- Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido 501-1193 Gifu, Japan
| | - Miho Kobayashi
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu, Gifu 501-1193, Japan; Life Science Research Center, Gifu University, Gifu, Gifu 501-1193, Japan; United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Gifu 501-1193, Japan
| | - Yuji O Kamatari
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu, Gifu 501-1193, Japan; Life Science Research Center, Gifu University, Gifu, Gifu 501-1193, Japan; United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Gifu 501-1193, Japan
| | - Tohru Mitsunaga
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Gifu 501-1193, Japan
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2
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Al-Warhi T, Elmaidomy AH, Maher SA, Abu-Baih DH, Selim S, Albqmi M, Al-Sanea MM, Alnusaire TS, Ghoneim MM, Mostafa EM, Hussein S, El-Damasy AK, Saber EA, Elrehany MA, Sayed AM, Othman EM, El-Sherbiny M, Abdelmohsen UR. The Wound-Healing Potential of Olea europaea L. Cv. Arbequina Leaves Extract: An Integrated In Vitro, In Silico, and In Vivo Investigation. Metabolites 2022; 12:metabo12090791. [PMID: 36144197 PMCID: PMC9503157 DOI: 10.3390/metabo12090791] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/04/2022] [Accepted: 08/12/2022] [Indexed: 11/17/2022] Open
Abstract
Olea europaea L. Cv. Arbequina (OEA) (Oleaceae) is an olive variety species that has received little attention. Besides our previous work for the chemical profiling of OEA leaves using LC−HRESIMS, an additional 23 compounds are identified. An excision wound model is used to measure wound healing action. Wounds are provided with OEA (2% w/v) or MEBO® cream (marketed treatment). The wound closure rate related to vehicle-treated wounds is significantly increased by OEA. Comparing to vehicle wound tissues, significant levels of TGF-β in OEA and MEBO® (p < 0.05) are displayed by gene expression patterns, with the most significant levels in OEA-treated wounds. Proinflammatory TNF-α and IL-1β levels are substantially reduced in OEA-treated wounds. The capability of several lignan-related compounds to interact with MMP-1 is revealed by extensive in silico investigation of the major OEA compounds (i.e., inverse docking, molecular dynamics simulation, and ΔG calculation), and their role in the wound-healing process is also characterized. The potential of OEA as a potent MMP-1 inhibitor is shown in subsequent in vitro testing (IC50 = 88.0 ± 0.1 nM). In conclusion, OEA is introduced as an interesting therapeutic candidate that can effectively manage wound healing because of its anti-inflammatory and antioxidant properties.
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Affiliation(s)
- Tarfah Al-Warhi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Abeer H. Elmaidomy
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62511, Egypt
| | - Sherif A. Maher
- Department of Biochemistry, Faculty of Pharmacy, Deraya University, New Minia 61111, Egypt
| | - Dalia H. Abu-Baih
- Department of Biochemistry, Faculty of Pharmacy, Deraya University, New Minia 61111, Egypt
| | - Samy Selim
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 72341, Saudi Arabia
| | - Mha Albqmi
- Chemistry Department, College of Science and Arts, Jouf University, Alqurayyat 77447, Saudi Arabia
| | - Mohammad M. Al-Sanea
- Pharmaceutical Chemistry Department, College of Pharmacy, Jouf University, Sakaka 72341, Saudi Arabia
- Correspondence: (M.M.A.-S.); (A.M.S.); (U.R.A.)
| | | | - Mohammed M. Ghoneim
- Pharmacognosy and Medicinal Plants Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
- Department of Pharmacy Practice, College of Pharmacy, Al Maarefa University, Ad Diriyah 13713, Saudi Arabia
| | - Ehab M. Mostafa
- Pharmacognosy and Medicinal Plants Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
- Department of Pharmacognosy, College of Pharmacy, Jouf University, Sakaka 72341, Saudi Arabia
| | - Shaimaa Hussein
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka 72341, Saudi Arabia
| | - Ashraf K. El-Damasy
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea
| | - Entesar Ali Saber
- Department of Histology and Cell Biology, Faculty of Medicine, Minia University, Minia 61519, Egypt
- Department of Histology and Cell Biology, Deraya University, Universities Zone, New Minia 61111, Egypt
| | - Mahmoud A. Elrehany
- Department of Biochemistry, Faculty of Pharmacy, Deraya University, New Minia 61111, Egypt
| | - Ahmed M. Sayed
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, Beni-Suef 62513, Egypt
- Correspondence: (M.M.A.-S.); (A.M.S.); (U.R.A.)
| | - Eman M. Othman
- Department of Biochemistry, Faculty of Pharmacy, Minia University, Minia 61519, Egypt
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Wuerzburg, Germany
| | - Mohamed El-Sherbiny
- Department of Basic Medical Sciences, College of Medicine, AlMaarefa University, Riyadh 11597, Saudi Arabia
- Department of Anatomy, Faculty of Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Usama Ramadan Abdelmohsen
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia 61519, Egypt
- Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, New Minia 61111, Egypt
- Correspondence: (M.M.A.-S.); (A.M.S.); (U.R.A.)
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3
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In Silico, In Vitro, and In Vivo Analysis of Tanshinone IIA and Cryptotanshinone from Salvia miltiorrhiza as Modulators of Cyclooxygenase-2/mPGES-1/Endothelial Prostaglandin EP3 Pathway. Biomolecules 2022; 12:biom12010099. [PMID: 35053247 PMCID: PMC8774285 DOI: 10.3390/biom12010099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/30/2021] [Accepted: 01/03/2022] [Indexed: 12/26/2022] Open
Abstract
Tanshinone IIA (TIIA) and cryptotanshinone (CRY) from Salvia miltiorrhiza Bunge were investigated for their inhibitory activity against the cyclooxygenase-2 (COX-2)/microsomal prostaglandin E synthase-1 (mPGES-1)/endothelial prostaglandin 3 (EP3) pathway using in silico, in vitro, in vivo, and ex vivo assays. From the analysis of the docking poses, both diterpenoids were able to interact significantly with COX-2, 5-lipoxygenase (5-LO), platelet-activating factor receptor (PAFR), and mPGES-1. This evidence was further corroborated by data obtained from a cell-free assay, where CRY displayed a significant inhibitory potency against mPGES-1 (IC50 = 1.9 ± 0.4 µM) and 5-LO (IC50 = 7.1 µM), while TIIA showed no relevant inhibition of these targets. This was consistent with their activity to increase mice bleeding time (CRY: 2.44 ± 0.13 min, p ≤ 0.001; TIIA: 2.07 ± 0.17 min p ≤ 0.01) and with the capability to modulate mouse clot retraction (CRY: 0.048 ± 0.011 g, p ≤ 0.01; TIIA: 0.068 ± 0.009 g, p ≤ 0.05). For the first time, our results show that TIIA and, in particular, CRY are able to interact significantly with the key proteins involved not only in the onset of inflammation but also in platelet activity (and hyper-reactivity). Future preclinical and clinical investigations, together with this evidence, could provide the scientific basis to consider these compounds as an alternative therapeutic approach for thrombotic- and thromboembolic-based diseases.
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4
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Cerofolini L, Fragai M, Luchinat C. Mechanism and Inhibition of Matrix Metalloproteinases. Curr Med Chem 2019; 26:2609-2633. [PMID: 29589527 DOI: 10.2174/0929867325666180326163523] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 03/06/2018] [Accepted: 03/06/2018] [Indexed: 01/02/2023]
Abstract
Matrix metalloproteinases hydrolyze proteins and glycoproteins forming the extracellular matrix, cytokines and growth factors released in the extracellular space, and membrane-bound receptors on the outer cell membrane. The pathological relevance of MMPs has prompted the structural and functional characterization of these enzymes and the development of synthetic inhibitors as possible drug candidates. Recent studies have provided a better understanding of the substrate preference of the different members of the family, and structural data on the mechanism by which these enzymes hydrolyze the substrates. Here, we report the recent advancements in the understanding of the mechanism of collagenolysis and elastolysis, and we discuss the perspectives of new therapeutic strategies for targeting MMPs.
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Affiliation(s)
- Linda Cerofolini
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Italy
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5
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Linder DP, Baker BE, Rodgers KR. [(H2O)Zn(Imidazole)n]2+: the vital roles of coordination number and geometry in Zn–OH2 acidity and catalytic hydrolysis. Phys Chem Chem Phys 2018; 20:24979-24991. [DOI: 10.1039/c8cp03121e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Zn(ii)–(Imidazole(ate))n coordination motif occurs in numerous biochemical systems, including carbonic anhydrase and the matrix metalloproteinases (MMPs).
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Affiliation(s)
- Douglas P. Linder
- Department of Chemistry and Physics
- Southwestern Oklahoma State University
- Weatherford
- USA
| | - Brett E. Baker
- Department of Chemistry and Physics
- Southwestern Oklahoma State University
- Weatherford
- USA
| | - Kenton R. Rodgers
- Department of Chemistry and Biochemistry
- North Dakota State University
- Fargo
- USA
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6
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Fabre B, Ramos A, de Pascual-Teresa B. Targeting Matrix Metalloproteinases: Exploring the Dynamics of the S1′ Pocket in the Design of Selective, Small Molecule Inhibitors. J Med Chem 2014; 57:10205-19. [DOI: 10.1021/jm500505f] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Benjamin Fabre
- Departamento de Química
y Bioquímica, Facultad de Farmacia, Universidad CEU San Pablo, Urbanización Monteprincipe, 28668 Madrid, Spain
| | - Ana Ramos
- Departamento de Química
y Bioquímica, Facultad de Farmacia, Universidad CEU San Pablo, Urbanización Monteprincipe, 28668 Madrid, Spain
| | - Beatriz de Pascual-Teresa
- Departamento de Química
y Bioquímica, Facultad de Farmacia, Universidad CEU San Pablo, Urbanización Monteprincipe, 28668 Madrid, Spain
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7
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Honarparvar B, Govender T, Maguire GEM, Soliman MES, Kruger HG. Integrated Approach to Structure-Based Enzymatic Drug Design: Molecular Modeling, Spectroscopy, and Experimental Bioactivity. Chem Rev 2013; 114:493-537. [DOI: 10.1021/cr300314q] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Bahareh Honarparvar
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Thavendran Govender
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Glenn E. M. Maguire
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Mahmoud E. S. Soliman
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Hendrik G. Kruger
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
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8
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Yadav MR, Murumkar PR, Zambre VP. Advances in studies on collagenase inhibitors. EXPERIENTIA SUPPLEMENTUM (2012) 2012; 103:83-135. [PMID: 22642191 DOI: 10.1007/978-3-0348-0364-9_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
Matrix metalloproteinases (MMPs) play an important role in many physiological and pathological processes. Development of MMP inhibitors, in particular collagenase inhibitors, for the treatment of arthritis has been more challenging, undoubtedly. Small-molecular-weight collagenase inhibitors may be classified into several different arbitrary structural classes, depending on the catalytic zinc-binding function as well as other structural elements of the inhibitors. This chapter tries to make an attempt in providing the reader with an overall flavor of the type of scaffolds reported in the past few years along with the molecular modeling studies.
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Affiliation(s)
- Mange Ram Yadav
- Pharmacy Department, The M.S. University of Baroda, Vadodara 390 001, Gujarat, India.
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9
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Abstract
BACKGROUND: Drug discovery is a complex and unpredictable endeavor with a high failure rate. Current trends in the pharmaceutical industry have exasperated these challenges and are contributing to the dramatic decline in productivity observed over the last decade. The industrialization of science by forcing the drug discovery process to adhere to assembly-line protocols is imposing unnecessary restrictions, such as short project time-lines. Recent advances in nuclear magnetic resonance are responding to these self-imposed limitations and are providing opportunities to increase the success rate of drug discovery. OBJECTIVE/METHOD: A review of recent advancements in NMR technology that have the potential of significantly impacting and benefiting the drug discovery process will be presented. These include fast NMR data collection protocols and high-throughput protein structure determination, rapid protein-ligand co-structure determination, lead discovery using fragment-based NMR affinity screens, NMR metabolomics to monitor in vivo efficacy and toxicity for lead compounds, and the identification of new therapeutic targets through the functional annotation of proteins by FAST-NMR. CONCLUSION: NMR is a critical component of the drug discovery process, where the versatility of the technique enables it to continually expand and evolve its role. NMR is expected to maintain this growth over the next decade with advancements in automation, speed of structure calculation, in-cell imaging techniques, and the expansion of NMR amenable targets.
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Affiliation(s)
- Robert Powers
- Department of Chemistry, University of Nebraska Lincoln, Lincoln, NE 68588
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10
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Torrance GM, Leader DP, Gilbert DR, Milner-White EJ. A novel main chain motif in proteins bridged by cationic groups: the niche. J Mol Biol 2008; 385:1076-86. [PMID: 19038265 DOI: 10.1016/j.jmb.2008.11.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2008] [Revised: 11/05/2008] [Accepted: 11/07/2008] [Indexed: 12/25/2022]
Abstract
We have surveyed the bridging of pairs of main chain carbonyl oxygens by cations or by delta(+) hydrogens within hydrogen bonding groups. A three to four residue motif, which we call the niche, with characteristic phi,psi angles, is by far the commonest feature with this property. The niche accommodates atoms or groups that offer delta(+) charges, including water molecules or metal ions, as well as amines, guanidines, and other NH(2) groups. Seven percent of all residues in an average soluble protein belong to a niche; another 7% have the niche conformation but no obvious bridging delta(+) group. Fifty-five percent of niches occur either following a type 1 beta-turn or at the C-termini of alpha-helices, and niches turn out to be the most common C-terminal features of alpha-helices: 39% of alpha-helical C-termini are niches, whereas 34% are Schellman loops. 3(10) helices also frequently terminate in niches. Niches that bind K(+), Na(+) or Ca(2+) occur in some functional contexts: in the cyclic peptides valinomycin and antamanide; in several enzymes that are allosterically activated by Na(+) or K(+); and in the calcium pump, where a niche is integrally involved in the ion transport.
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Affiliation(s)
- Gilleain M Torrance
- Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
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11
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Bhaskaran R, Palmier MO, Bagegni NA, Liang X, Van Doren SR. Solution structure of inhibitor-free human metalloelastase (MMP-12) indicates an internal conformational adjustment. J Mol Biol 2007; 374:1333-44. [PMID: 17997411 DOI: 10.1016/j.jmb.2007.10.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2007] [Revised: 09/30/2007] [Accepted: 10/08/2007] [Indexed: 10/22/2022]
Abstract
Macrophage metalloelastase or matrix metalloproteinase-12 (MMP-12) appears to exacerbate atherosclerosis, emphysema, aortic aneurysm, rheumatoid arthritis, and inflammatory bowel disease. An inactivating E219A mutation, validated by crystallography and NMR spectra, prevents autolysis of MMP-12 and allows us to determine its NMR structure without an inhibitor. The structural ensemble of the catalytic domain without an inhibitor is based on 2813 nuclear Overhauser effects (NOEs) and has an average RMSD to the mean structure of 0.25 A for the backbone and 0.61 A for all heavy atoms for residues Trp109-Gly263. Compared to crystal structures of MMP-12, helix B (hB) at the active site is unexpectedly more deeply recessed under the beta-sheet. This opens a pocket between hB and beta-strand IV in the active-site cleft. Both hB and an internal cavity are shifted toward beta-strand I, beta-strand III, and helix A on the back side of the protease. About 25 internal NOE contacts distinguish the inhibitor-free solution structure and indicate hB's greater depth and proximity to the sheet and helix A. Line broadening and multiplicity of amide proton NMR peaks from hB are consistent with hB undergoing a slow conformational exchange among subtly different environments. Inhibitor-binding-induced perturbations of the NMR spectra of MMP-1 and MMP-3 map to similar locations across MMP-12 and encompass the internal conformational adjustments. Evolutionary trace analysis suggests a functionally important network of residues that encompasses most of the locations adjusting in conformation, including 18 residues with NOE contacts unique to inhibitor-free MMP-12. The conformational change, sequence analysis, and inhibitor perturbations of NMR spectra agree on the network they identify between structural scaffold and the active site of MMPs.
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Affiliation(s)
- Rajagopalan Bhaskaran
- Department of Biochemistry, 117 Schweitzer Hall, University of Missouri, Columbia, MO 65211, USA
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12
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Arendt Y, Banci L, Bertini I, Cantini F, Cozzi R, Del Conte R, Gonnelli L. Catalytic domain of MMP20 (Enamelysin) - the NMR structure of a new matrix metalloproteinase. FEBS Lett 2007; 581:4723-6. [PMID: 17869250 DOI: 10.1016/j.febslet.2007.08.069] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Revised: 08/24/2007] [Accepted: 08/27/2007] [Indexed: 11/28/2022]
Abstract
The solution structure of the catalytic domain of MMP-20, a member of the matrix metalloproteinases family not yet structurally characterized, complexed with N-Isobutyl-N-(4-methoxyphenylsulfonyl)glycyl hydroxamic acid (NNGH), is here reported and compared with other MMPs-NNGH adducts. The backbone dynamic has been characterized as well. We have found that, despite the same fold and very high overall similarity, the present structure experiences specific structural and dynamical similarities with some MMPs and differences with others, around the catalytic cavity. The present solution structure, not only contributes to fill the gap of structural knowledge on human MMPs, but also provides further information to design more selective and efficient inhibitors for a specific member of this class of proteins.
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Affiliation(s)
- Yvonne Arendt
- ProtEra S.r.l., Via delle Idee 22, 50019 Sesto Fiorentino (FI), Italy
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13
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Todorov NP, Buenemann CL, Alberts IL. De novo ligand design to an ensemble of protein structures. Proteins 2006; 64:43-59. [PMID: 16555306 DOI: 10.1002/prot.20928] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We describe a combinatorial method for de novo ligand design to an ensemble of receptor structures. Receptor conformations, protonation states, and structural water molecules are considered consistently within the framework of de novo ligand design. The method relies on Monte Carlo optimization to search the space of ligand structures, conformations, and rigid-body movements as well as receptor models. The method is applied to an ensemble of HIV protease and human collagenase receptor models. Ligand structures generated de novo exhibit the correct hydrogen-bonding pattern in the core of the active site, with hydrophobic groups extending into the receptor S1 and S1' pocket space. Furthermore, it is shown that known ligands are recovered in the correct binding mode and in the native, most tightly binding receptor model.
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Affiliation(s)
- N P Todorov
- De Novo Pharmaceuticals Ltd., Compass House, Cambridge, United Kingdom
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14
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Cuniasse P, Devel L, Makaritis A, Beau F, Georgiadis D, Matziari M, Yiotakis A, Dive V. Future challenges facing the development of specific active-site-directed synthetic inhibitors of MMPs. Biochimie 2005; 87:393-402. [PMID: 15781327 DOI: 10.1016/j.biochi.2004.09.025] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2004] [Accepted: 09/23/2004] [Indexed: 11/24/2022]
Abstract
Despite a deep knowledge on the 3D-structure of several catalytic domains of MMPs, the development of highly specific synthetic active-site-directed inhibitors of MMPs, able to differentiate the different members of this protease family, remains a strong challenge. Due to the flexible nature of MMP active-site, the development of specific MMP inhibitors will need to combine sophisticated theoretical and experimental approaches to decipher in each MMP the specific structural and dynamic features that can be exploited to obtain the desired selectivity.
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Affiliation(s)
- P Cuniasse
- CEA, Département d'Ingénierie et d'Etudes des Protéines (DIEP), CE-Saclay, 91191 Gif/Yvette cedex, France
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15
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Svab I, Alexandru D, Vitos G, Flonta ML. Binding affinities for sulfonamide inhibitors with matrix metalloproteinase-2 using a linear response method. J Cell Mol Med 2005; 8:551-62. [PMID: 15601584 PMCID: PMC6740266 DOI: 10.1111/j.1582-4934.2004.tb00480.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Due to their involvement in many pathological conditions, matrix metalloproteinases (MMPs), are very attractive therapeutic targets. Our study focuses on one of them, MMP-2, which is involved in tumor progression and metastasis. Recently, the solution structure of the catalytic domain of MMP-2 complexed with a hydroxamic acid inhibitor (SC-74020) was published by Feng et al. Using the Hanessian group published binding affinity data and the structure published by Feng as a basis, we have built a binding affinity model by targeting the S(2)' pocket of the enzyme with a set of nine alpha-N-sulfonylamino hydroxamic acid derivatives. Two binding geometries of each ligand have been generated corresponding to two binding modes denoted A and B, respectively, of which the first one is targeting the S(2)' pocket and the second one the S(1) pocket. For the binding affinity model developed for mode A the computed activities show a rmsd of 0.583 kcal/mol as compared with the experimental data, and a correlation coefficient r(2) of 0.779, while in the case of the binding mode B a rmsd of 0.834 kcal/mol and correlation coefficient r(2) of 0.500, respectively, were obtained. In conclusion, our data suggest a higher probability for the Phe(76) gated S(2)' open form pocket to accommodate the substituent alpha versus the wide solvent exposed S(1) subsite, probability which some research groups could have overlooked due to extensive use in their calculations of non revealing S(2)' pocket open state crystallographic structures instead of NMR ones.
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Affiliation(s)
- I Svab
- Nicolae Simionescu Institute of Cellular Biology and Pathology 8, B.P. Haseu Street, Bucharest, 79691, Romania.
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16
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Sørensen MD, Blaehr LKA, Christensen MK, Høyer T, Latini S, Hjarnaa PJV, Björkling F. Cyclic phosphinamides and phosphonamides, novel series of potent matrix metalloproteinase inhibitors with antitumour activity. Bioorg Med Chem 2003; 11:5461-84. [PMID: 14642591 DOI: 10.1016/j.bmc.2003.09.015] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The design, synthesis, and structure-activity relationship (SAR) of a series of novel nonpeptidic cyclic phosphon- and phosphinamide-based hydroxamic acids as inhibitors of matrix metalloproteinases MMP-1, MMP-3, and MMP-9 are presented. Based on modelling studies and X-ray analysis, a model of the binding mode of these novel compounds in the MMP active site was obtained. This model provided a rational explanation for the observed SAR data, which included a systematic study of different S1' directed substituents, zinc-complexing groups, chirality, and variation of the cyclic phosphon- and phosphinamide rings. The in vivo effect of four compounds in a human fibrosarcoma mouse model (HT1080) was evaluated and compared to that of a reference compound, Prinomastat. Inhibition of tumour growth was observed for all four compounds.
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Affiliation(s)
- Morten Dahl Sørensen
- Medicinal Chemistry Research, LEO Pharma, Industriparken 55, DK-2750 Ballerup, Denmark.
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17
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Powers R. Applications of NMR to structure-based drug design in structural genomics. JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS 2003; 2:113-23. [PMID: 12836668 DOI: 10.1023/a:1020445506369] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Structural genomics is poised to have a tremendous impact on traditional structure-based drug design programs. As a result, there is a growing need to obtain rapid structural information in a reliable form that is amenable to rational drug design. In this manner, NMR has been expanding and evolving its role in aiding the design process. A variety of NMR methodologies that cover a range of inherent resolution are described in the context of structure-based drug design in the era of structural genomics.
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Affiliation(s)
- Robert Powers
- Department of Biological Chemistry, Wyeth Research, 87 Cambridge Park Dr., Cambridge, Massachusetts 02140, USA.
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18
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Abstract
Side-chain flexibility of ligand-binding sites needs to be considered in the rational design of novel inhibitors. We have developed a method to generate conformational ensembles that efficiently sample local side-chain flexibility from a single crystal structure. The rotamer-based approach is tested here for the S1' pocket of human collagenase-1 (MMP-1), which is known to undergo conformational changes in multiple side-chains upon binding of certain inhibitors. First, a raw ensemble consisting of a large number of conformers of the S1' pocket was generated using an exhaustive search of rotamer combinations on a template crystal structure. A combination of principal component analysis and fuzzy clustering was then employed to successfully identify a core ensemble consisting of a low number of representatives from the raw ensemble. The core ensemble contained geometrically diverse conformers of stable nature, as indicated in several cases by a relative energy lower than that of the minimised template crystal structure. Through comparisons with X-ray crystallography and NMR structural data we show that the core ensemble occupied a conformational space similar to that observed under experimental conditions. The synthetic inhibitor RS-104966 is known to induce a conformational change in the side-chains of the S1' pocket of MMP-1 and could not be docked in the template crystal structure. However, the experimental binding mode was reproduced successfully using members of the core ensemble as the docking target, establishing the usefulness of the method in drug design.
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Affiliation(s)
- Per Källblad
- Department of Pharmacology, Tennis Court Road, Cambridge CB2 1QJ, UK.
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19
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Feng Y, Likos JJ, Zhu L, Woodward H, Munie G, McDonald JJ, Stevens AM, Howard CP, De Crescenzo GA, Welsch D, Shieh HS, Stallings WC. Solution structure and backbone dynamics of the catalytic domain of matrix metalloproteinase-2 complexed with a hydroxamic acid inhibitor. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1598:10-23. [PMID: 12147339 DOI: 10.1016/s0167-4838(02)00307-2] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
MMP-2 is a member of the matrix metalloproteinase family that has been implicated in tumor cell metastasis and angiogenesis. Here, we describe the solution structure of a catalytic domain of MMP-2 complexed with a hydroxamic acid inhibitor (SC-74020), determined by three-dimensional heteronuclear NMR spectroscopy. The catalytic domain, designated MMP-2C, has a short peptide linker replacing the internal fibronectin-domain insertion and is enzymatically active. Distance geometry-simulated annealing calculations yielded 14 converged structures with atomic root-mean-square deviations (r.m.s.d.) of 1.02 and 1.62 A from the mean coordinate positions for the backbone and for all heavy atoms, respectively, when 11 residues at the N-terminus are excluded. The structure has the same global fold as observed for other MMP catalytic domains and is similar to previously solved crystal structures of MMP-2. Differences observed between the solution and the crystal structures, near the bottom of the S1' specificity loop, appear to be induced by the large inhibitor present in the solution structure. The MMP-2C solution structure is compared with MMP-8 crystal structure bound to the same inhibitor to highlight the differences especially in the S1' specificity loop. The finding provides a structural explanation for the selectivity between MMP-2 and MMP-8 that is achieved by large inhibitors.
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Affiliation(s)
- Yiqing Feng
- Discovery Research, Pharmacia Corporation, 700 Chesterfield Parkway North, St. Louis, MO 63017, USA.
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20
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Nar H, Werle K, Bauer MM, Dollinger H, Jung B. Crystal structure of human macrophage elastase (MMP-12) in complex with a hydroxamic acid inhibitor. J Mol Biol 2001; 312:743-51. [PMID: 11575929 DOI: 10.1006/jmbi.2001.4953] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Human macrophage elastase (MMP-12) is a member of the family of matrix metalloproteinases (MMPs) that plays, like other members of the family, an important role in inflammatory processes contributing to tissue remodelling and destruction. In particular, a prominent role of MMP-12 in the destruction of elastin in the lung alveolar wall and the pathogenesis of emphysema has been suggested. It is therefore an attractive therapeutic target. We describe here the crystal structure of the catalytic domain of MMP-12 in complex with a hydroxamic acid inhibitor, CGS27023A. MMP-12 adopts the typical MMP fold and binds a structural zinc ion and three calcium ions in addition to the catalytic zinc ion. The enzyme structure shows an ordered N terminus close to the active site that is identical in conformation with the superactivated form of MMP-8. The S1'-specificity pocket is large and extends into a channel through the protein, which puts MMP-12 into the class of MMPs 3, 8 and 13 with large and open specificity pockets. The two crystallographically independent molecules adopt different conformations of the S1'-loop and its neighbouring loop due to differing crystal packing environments, suggesting that flexibility or the possibility of structural adjustments of these loop segments are intrinsic features of the MMP-12 structure and probably a common feature for all MMPs. The inhibitor binds in a bidentate fashion to the catalytic zinc ion. Its polar groups form hydrogen bonds in a substrate-like manner with beta-strand sIV of the enzyme, while the hydrophobic substituents are either positioned on the protein surface and are solvent-exposed or fill the upper part of the specificity pocket. The present structure enables us to aid the design of potent and selective inhibitors for MMP-12.
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Affiliation(s)
- H Nar
- Department of Medicinal Chemistry, Boehringer Ingelheim Pharma KG, Biberach, Germany.
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21
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Moy FJ, Chanda PK, Chen JM, Cosmi S, Edris W, Levin JI, Powers R. High-resolution solution structure of the catalytic fragment of human collagenase-3 (MMP-13) complexed with a hydroxamic acid inhibitor. J Mol Biol 2000; 302:671-89. [PMID: 10986126 DOI: 10.1006/jmbi.2000.4082] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The high-resolution solution structure of the catalytic fragment of human collagenase-3 (MMP-13) complexed with a sulfonamide derivative of a hydroxamic acid compound (WAY-151693) has been determined by multidimensional heteronuclear NMR. A total of 30 structures were calculated for residues 7-164 by means of hybrid distance geometry-simulated annealing using a total of 3280 experimental NMR restraints. The atomic rms distribution about the mean coordinate positions for the 30 structures is 0.43(+/-0.05) A for the backbone atoms, 0.80(+/-0.09) A for all atoms, and 0.47(+/-0.04) A for all atoms excluding disordered side-chains. The overall structure of MMP-13 is composed of a beta-sheet consisting of five beta-strands in a mixed parallel and anti-parallel arrangement and three alpha-helices where its overall fold is consistent with previously solved MMP structures. A comparison of the NMR structure of MMP-13 with the published 1.6 A resolution X-ray structure indicates that the major differences between the structures is associated with loop dynamics and crystal-packing interactions. The side-chains of some active-site residues for the NMR and X-ray structures of MMP-13 adopt distinct conformations. This is attributed to the presence of unique inhibitors in the two structures that encounter distinct interactions with MMP-13. The major structural difference observed between the MMP-13 and MMP-1 NMR structures is the relative size and shape of the S1' pocket where this pocket is significantly longer for MMP-13, nearly reaching the surface of the protein. Additionally, MMP-1 and MMP-13 exhibit different dynamic properties for the active-site loop and the structural Zn-binding region. The inhibitor WAY-151693 is well defined in the MMP-13 active-site based on a total of 52 distance restraints. The binding motif of WAY-151693 in the MMP-13 complex is consistent with our previously reported MMP-1:CGS-27023A NMR structure and is similar to the MMP-13: RS-130830 X-ray structure.
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Affiliation(s)
- F J Moy
- Department of Biological Chemistry, Wyeth Research, 85 Bolton St., Cambridge, MA 02140, USA
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22
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Zhang X, Gonnella NC, Koehn J, Pathak N, Ganu V, Melton R, Parker D, Hu SI, Nam KY. Solution structure of the catalytic domain of human collagenase-3 (MMP-13) complexed to a potent non-peptidic sulfonamide inhibitor: binding comparison with stromelysin-1 and collagenase-1. J Mol Biol 2000; 301:513-24. [PMID: 10926524 DOI: 10.1006/jmbi.2000.3988] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The full three-dimensional structure of the catalytic domain of human collagenase-3 (MMP-13) complexed to a potent, sulfonamide hydroxamic acid inhibitor (CGS 27023) has been determined by NMR spectroscopy. The results reveal a core domain for the protein consisting of three alpha-helices and five beta-sheet strands with an overall tertiary fold similar to the catalytic domains of other matrix metalloproteinase family members. The S1' pocket, which is the major site of hydrophobic binding interaction, was found to be a wide cleft spanning the length of the protein and presenting facile opportunity for inhibitor extension deep into the pocket. Comparison with the reported X-ray structure of collagenase-3 showed evidence of flexibility for the loop region flanking the S1' pocket in both NMR and X-ray data. This flexibility was corroborated by NMR dynamics studies. Inhibitor binding placed the methoxy phenyl ring in the S1' pocket with the remainder of the molecule primarily solvent-exposed. The binding mode for this inhibitor was found to be similar with respect to stromelysin-1 and collagenase-1; however, subtle comparative differences in the interactions between inhibitor and enzyme were observed for the three MMPs that were consistent with their respective binding potencies.
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Affiliation(s)
- X Zhang
- Novartis Institute for Biomedical Research, 556 Morris Ave., Summit, NJ 07901, USA
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23
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Scozzafava A, Ilies MA, Manole G, Supuran CT. Protease inhibitors. Part 12. Synthesis of potent matrix metalloproteinase and bacterial collagenase inhibitors incorporating sulfonylated N-4-nitrobenzyl-beta-alanine hydroxamate moieties. Eur J Pharm Sci 2000; 11:69-79. [PMID: 10913755 DOI: 10.1016/s0928-0987(00)00089-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
N-4-Nitrobenzyl-beta-alanine was reacted with alkyl/arylsulfonyl halides, followed by conversion of the COOH to the CONHOH group. Structurally related compounds were obtained by reaction of N-4-nitrobenzyl-beta-alanine with aryl isocyanates, arylsulfonyl isocyanates or benzoyl isothiocyanate, followed by similar conversion of the COOH into the CONHOH moiety. Another subseries of derivatives was prepared from sulfanilyl- or metanilyl-4-nitrobenzyl-beta-alanine by reaction with arylsulfonyl isocyanates, followed by the introduction of the hydroxamate moiety. The new compounds were assayed as inhibitors of four matrix metalloproteinases (MMPs), MMP-1, MMP-2, MMP-8 and MMP-9, and of the Clostridium histolyticum collagenase (ChC). Some of the prepared hydroxamate derivatives proved to be very effective collagenase/gelatinase inhibitors, depending on the substitution pattern at the sulfonamido moiety. Substitutions leading to the best inhibitors of MMP-1, a short-pocket enzyme, were those involving pentafluorophenylsulfonyl or 3-trifluoromethyl-phenylsulfonyl at P(1') (K(I) of 3-5 nM). For MMP-2, MMP-8 and MMP-9 (deep-pocket enzymes), the best inhibitors were those containing perfluoroalkylsulfonyl- and substituted-arylsulfonyl moieties, such as pentafluorophenylsulfonyl, 3- and 4-protected-aminophenylsulfonyl-, 3- and 4-carboxy-phenylsulfonyl-, arylsulfonylureido- or arylsulfonylureido-sulfanilyl-/metanilyl moieties at P(1'). Bulkier groups in this position, such as 1- and 2-naphthyl-, substituted-naphthyl or quinoline-8-yl- moieties, among others, led to less effective MMP/ChC inhibitors. The best ChC inhibitors were again those containing pentafluorophenylsulfonyl, 3- and 4-protected-aminophenylsulfonyl P(1') groups. This study demonstrates that the 4-nitrobenzyl moiety, investigated here for the first time, is an efficient P(2') anchoring moiety, whereas the beta-alanyl scaffold can successfully replace the alpha-amino acyl one, for obtaining potent MMP/ChC inhibitors.
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Affiliation(s)
- A Scozzafava
- Università degli Studi, Laboratorio di Chimica Inorganica e Bioinorganica, Florence, Italy
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24
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Braslau R, Axon JR, Lee B. Synthesis of N-hydroxy peptides: chemical ligation of O-acyl hydroxamic acids. Org Lett 2000; 2:1399-401. [PMID: 10814457 DOI: 10.1021/ol005722+] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[process--see text] A novel chemical ligation process is described that results in the construction of N-hydroxy peptides.
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Affiliation(s)
- R Braslau
- Department of Chemistry, University of California, Santa Cruz, California 95064, USA.
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