1
|
Ancajas CMF, Oyedele AS, Butt CM, Walker AS. Advances, opportunities, and challenges in methods for interrogating the structure activity relationships of natural products. Nat Prod Rep 2024. [PMID: 38912779 DOI: 10.1039/d4np00009a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Time span in literature: 1985-early 2024Natural products play a key role in drug discovery, both as a direct source of drugs and as a starting point for the development of synthetic compounds. Most natural products are not suitable to be used as drugs without further modification due to insufficient activity or poor pharmacokinetic properties. Choosing what modifications to make requires an understanding of the compound's structure-activity relationships. Use of structure-activity relationships is commonplace and essential in medicinal chemistry campaigns applied to human-designed synthetic compounds. Structure-activity relationships have also been used to improve the properties of natural products, but several challenges still limit these efforts. Here, we review methods for studying the structure-activity relationships of natural products and their limitations. Specifically, we will discuss how synthesis, including total synthesis, late-stage derivatization, chemoenzymatic synthetic pathways, and engineering and genome mining of biosynthetic pathways can be used to produce natural product analogs and discuss the challenges of each of these approaches. Finally, we will discuss computational methods including machine learning methods for analyzing the relationship between biosynthetic genes and product activity, computer aided drug design techniques, and interpretable artificial intelligence approaches towards elucidating structure-activity relationships from models trained to predict bioactivity from chemical structure. Our focus will be on these latter topics as their applications for natural products have not been extensively reviewed. We suggest that these methods are all complementary to each other, and that only collaborative efforts using a combination of these techniques will result in a full understanding of the structure-activity relationships of natural products.
Collapse
Affiliation(s)
| | | | - Caitlin M Butt
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
| | - Allison S Walker
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| |
Collapse
|
2
|
Qiao S, Cheng Z, Li F. Chemoenzymatic synthesis of macrocyclic peptides and polyketides via thioesterase-catalyzed macrocyclization. Beilstein J Org Chem 2024; 20:721-733. [PMID: 38590533 PMCID: PMC10999997 DOI: 10.3762/bjoc.20.66] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/21/2024] [Indexed: 04/10/2024] Open
Abstract
Chemoenzymatic strategies that combine synthetic and enzymatic transformations offer efficient approaches to yield target molecules, which have been increasingly employed in the synthesis of bioactive natural products. In the biosynthesis of macrocyclic nonribosomal peptides, polyketides, and their hybrids, thioesterase (TE) domains play a significant role in late-stage macrocyclization. These domains can accept mimics of native substrates in vitro and exhibit potential for use in total synthesis. This review summarizes the recent advances of TE domains in the chemoenzymatic synthesis for these natural products that aim to address the common issues in classical synthetic approaches and increase synthetic efficiencies, which have the potential to facilitate further pharmaceutical research.
Collapse
Affiliation(s)
- Senze Qiao
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Zhongyu Cheng
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Fuzhuo Li
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, China
- Key Laboratory of Smart Drug Delivery (Ministry of Education), State Key Laboratory of Medical Neurobiology, Fudan University, Shanghai, 201203, China
| |
Collapse
|
3
|
Moreira R, Taylor SD. A54145 Factor D Is Not Less Susceptible to Inhibition by Lung Surfactant than Daptomycin. ACS Infect Dis 2022; 8:1935-1947. [PMID: 36001599 DOI: 10.1021/acsinfecdis.2c00313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A54145 factor D (A5D) is a cyclic lipopeptide antibiotic that shares several structural and mechanistic features with the clinically important antibiotic daptomycin, such as their requirement for calcium and phosphatidylglycerol (PG) for activity. Studies by others have suggested that daptomycin's activity is strongly inhibited by lung surfactant while A5D's activity is not. This finding has inspired efforts, albeit unsuccessful, to develop an A5D analogue that is highly active in the presence of lung surfactant and can be used for treating community acquired pneumonia (CAP). Here we demonstrate that A5D, like daptomycin, has a strong preference for the 1,2-diacyl-sn-glycero-3-phospho-1'-sn-glycerol stereoisomer (2R,2'S configuration) of PG. This PG stereoisomer was determined to be the only stereoisomer of PG in lung surfactant. Both antibiotics are completely antagonized by approximately 1-2 mol equiv of 2R,2'S-PG. Studies performed in the presence of lung surfactant revealed that the antagonism of these peptides by surfactant is mainly due to their interaction with PG and that A5D is not significantly less susceptible to inhibition by lung surfactant than daptomycin.
Collapse
Affiliation(s)
- Ryan Moreira
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Scott D Taylor
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| |
Collapse
|
4
|
Taylor SD. A Decade of Research on Daptomycin. Synlett 2022. [DOI: 10.1055/a-1885-4934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
AbstractDaptomycin is a calcium-dependent cyclic lipodepsipeptide antibiotic that is used in the clinic for treating serious infections caused by Gram-positive bacteria. In this account, I present a summary of the research that has been conducted in my group on daptomycin’s total chemical synthesis, its structure–activity relationships, and its mechanism of action, since we began our studies a decade ago.1 Introduction2 Solid-Phase Synthesis of Daptomycin by an On-Resin Cyclization3 α-Azido Acids and Alternative Routes to Daptomycin by On-Resin Cyclization4 Synthesis of Daptomycin by an Off-Resin Cyclization5 SAR Studies on Daptomycin6 Oligomerization of Daptomycin on Membranes7 The Chiral Target of Daptomycin8 SAR Studies on Phosphatidylglycerol9 Conclusions
Collapse
|
5
|
Moreira R, Taylor SD. Establishing the Structure-Activity Relationship between Phosphatidylglycerol and Daptomycin. ACS Infect Dis 2022; 8:1674-1686. [PMID: 35793519 DOI: 10.1021/acsinfecdis.2c00262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Daptomycin is a clinical antibiotic used to treat serious infections caused by Gram-positive bacteria. Although there is debate about the action mechanism of daptomycin, it is known that daptomycin requires both calcium and phosphatidylglycerol (PG) to exert its antibacterial effect. Despite the importance and uniqueness of the interaction of daptomycin with PG, very little is known about this interaction or the nascent daptomycin-PG complex. In this work, we establish a structure-activity relationship between daptomycin and PG through the synthesis of PG analogues. In total, nine PGs were synthesized using a divergent approach employing phosphoramidite chemistry. The interaction between daptomycin and these PGs was studied using fluorescence, circular dichroism, and isothermal titration calorimetry. It was determined that daptomycin is highly sensitive to the modification of the headgroup of PG and both hydroxyl groups influence membrane binding, oligomerization, and backbone structure. Methylation of each hydroxyl in the headgroup suggests that the binding pocket envelops both hydroxyl groups. A PG acyl tail chain length of at least 7-8 carbons is required for stoichiometric binding at micromolar peptide concentrations. Daptomycin binds to PG having 8-carbon, linear, unsaturated acyl groups (C8PGs) at the micromolar concentration and interacts with C8PG in essentially the same manner as when the PG is incorporated into a liposome, and thus, preassembly of individual PG moieties is not a prerequisite for binding, structural transition, and oligomerization.
Collapse
Affiliation(s)
- Ryan Moreira
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Scott D Taylor
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| |
Collapse
|
6
|
Barnawi G, Noden M, Goodyear J, Marlyn J, Schneider O, Beriashvili D, Schulz S, Moreira R, Palmer M, Taylor SD. Discovery of Highly Active Derivatives of Daptomycin by Assessing the Effect of Amino Acid Substitutions at Positions 8 and 11 on a Daptomycin Analogue. ACS Infect Dis 2022; 8:778-789. [PMID: 35317552 DOI: 10.1021/acsinfecdis.1c00483] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Daptomycin is an important antibiotic used for treating serious infections caused by Gram-positive bacteria including methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci. Establishing structure-activity relationships of daptomycin is important for developing new daptomycin-based antibiotics with expanded clinical applications and for tackling the ever-increasing problem of antimicrobial resistance. Toward this end, Dap-K6-E12-W13, an active analogue of daptomycin in which the uncommon amino acids in daptomycin are replaced with their common counterparts, was used as a model system for studying the effect of amino acid variation at positions 8 and 11 on in vitro biological activity against a model organism, Bacillus subtilis, and calcium-dependent insertion into model membranes. None of the new peptides were more active than Dap-K6-E12-W13; however, substitution at positions 8 and/or 11 with cationic residues resulted in little or no loss of activity, and some of these analogues were able to insert into model membranes at lower calcium ion concentrations than the parent peptide. Incorporation of these cationic residues into positions 8 and/or 11 of daptomycin itself yielded some derivatives that exhibited lower minimum inhibitory concentrations than daptomycin against B. subtilis 1046 as well as comparable and sometimes superior activity against clinical isolates of MRSA.
Collapse
Affiliation(s)
- Ghufran Barnawi
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Michael Noden
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Jeremy Goodyear
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Julian Marlyn
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Olivia Schneider
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - David Beriashvili
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Sarah Schulz
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Ryan Moreira
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Michael Palmer
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Scott D. Taylor
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| |
Collapse
|
7
|
Moreira R, Taylor SD. The Chiral Target of Daptomycin Is the 2
R
,2′
S
Stereoisomer of Phosphatidylglycerol. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202114858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ryan Moreira
- Deptartment of Chemistry University of Waterloo 200 University Ave. West Waterloo Ontario Canada
| | - Scott D. Taylor
- Deptartment of Chemistry University of Waterloo 200 University Ave. West Waterloo Ontario Canada
| |
Collapse
|
8
|
Moreira R, Taylor SD. The Chiral Target of Daptomycin Is the 2R,2'S Stereoisomer of Phosphatidylglycerol. Angew Chem Int Ed Engl 2021; 61:e202114858. [PMID: 34843157 DOI: 10.1002/anie.202114858] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Indexed: 12/12/2022]
Abstract
Daptomycin (dap) is an important antibiotic that interacts with the bacterial membrane lipid phosphatidylglycerol (PG) in a calcium-dependent manner. The enantiomer of dap (ent-dap) was synthesized and was found to be 85-fold less active than dap against B. subtilis, indicating that dap interacts with a chiral target as part of its mechanism of action. Using liposomes containing enantiopure PG, we demonstrate that the binding of dap to PG, the structural transition that occurs upon dap binding to PG, and the subsequent oligomerization of dap, depends upon the configuration of PG, and that dap prefers the 1,2-diacyl-sn-glycero-3-phospho-1'-sn-glycerol stereoisomer (2R,2'S configuration). Ent-dap has a lower affinity for 2R,2'S liposomes than dap and cannot oligomerize to the same extent as dap, which accounts for why ent-dap is less active than dap. To our knowledge, this is the first example whereby the activity of an antibiotic depends upon the configuration of a lipid head group.
Collapse
Affiliation(s)
- Ryan Moreira
- Deptartment of Chemistry, University of Waterloo, 200 University Ave. West, Waterloo, Ontario, Canada
| | - Scott D Taylor
- Deptartment of Chemistry, University of Waterloo, 200 University Ave. West, Waterloo, Ontario, Canada
| |
Collapse
|
9
|
Kotsogianni I, Wood TM, Alexander FM, Cochrane SA, Martin NI. Binding Studies Reveal Phospholipid Specificity and Its Role in the Calcium-Dependent Mechanism of Action of Daptomycin. ACS Infect Dis 2021; 7:2612-2619. [PMID: 34406007 PMCID: PMC8438661 DOI: 10.1021/acsinfecdis.1c00316] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Multidrug-resistant bacteria pose a serious global health threat as antibiotics are increasingly losing their clinical efficacy. A molecular level understanding of the mechanism of action of antimicrobials plays a key role in developing new agents to combat the threat of antimicrobial resistance. Daptomycin, the only clinically used calcium-dependent lipopeptide antibiotic, selectively disrupts Gram-positive bacterial membranes to illicit its bactericidal effect. In this study, we use isothermal titration calorimetry to further characterize the structural features of the target bacterial phospholipids that drive daptomycin binding. Our studies reveal that daptomycin shows a clear preference for the phosphoglycerol headgroup. Furthermore, unlike other calcium-dependent lipopeptide antibiotics, calcium binding by daptomycin is strongly dependent on the presence of phosphatidylglycerol. These investigations provide new insights into daptomycin's phospholipid specificity and calcium binding behavior.
Collapse
Affiliation(s)
- Ioli Kotsogianni
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Thomas M. Wood
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Francesca M. Alexander
- School of Chemistry and Chemical Engineering, David Keir Building, Stranmillis Road, Queen’s University Belfast, Belfast, BT9 5AG, United Kingdom
| | - Stephen A. Cochrane
- School of Chemistry and Chemical Engineering, David Keir Building, Stranmillis Road, Queen’s University Belfast, Belfast, BT9 5AG, United Kingdom
| | - Nathaniel I. Martin
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| |
Collapse
|
10
|
Noden M, Taylor SD. Enantioselective Synthesis and Application of Small and Environmentally Sensitive Fluorescent Amino Acids for Probing Biological Interactions. J Org Chem 2021; 86:11407-11418. [PMID: 34387500 DOI: 10.1021/acs.joc.1c00907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Environmentally sensitive fluorescent amino acids (FlAAs) have been used extensively to probe biological interactions. However, most of these amino acids are large and do not resemble amino acid side chains. Here, we report the enantioselective synthesis of two small and environmentally sensitive fluorescent amino acids bearing 7-dialkylaminocoumarin side chains by alkylation of a Ni(II) glycine Schiff base complex. These amino acids exhibit a large increase in fluorescence as environment polarity decreases. One of these FLAAs was incorporated into a highly active analog of the cyclic lipopeptide antibiotic paenibacterin by Fmoc solid-phase peptide synthesis via a new and very efficient route. This peptide was used to probe the interaction of the antibiotic with model liposomes, lipopolysaccharides, and live bacteria.
Collapse
Affiliation(s)
- Michael Noden
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Scott D Taylor
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| |
Collapse
|
11
|
Moreira R, Wolfe J, Taylor SD. A high-yielding solid-phase total synthesis of daptomycin using a Fmoc SPPS stable kynurenine synthon. Org Biomol Chem 2021; 19:3144-3153. [PMID: 33508054 DOI: 10.1039/d0ob02504f] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A high-yielding total synthesis of daptomycin, an important clinical antibiotic, is described. Key to the development of this synthesis was the elucidation of a Camps cyclization reaction that occurs in the solid-phase when conventionally used kynurenine (Kyn) synthons, such as Fmoc-l-Kyn(Boc,CHO)-OH and Fmoc-l-Kyn(CHO,CHO)-OH, are exposed to 20% 2-methylpiperidine (2MP)/DMF. During the synthesis of daptomycin, this side reaction was accompanied by intractable peptide decomposition, which resulted in a low yield of Dap and a 4-quinolone containing peptide. The Camps cyclization was found to occur in solution when Boc-l-Kyn(Boc,CHO)-Ot-Bu and Boc-l-Kyn(CHO,CHO)-OMe were exposed to 20% 2MP/DMF giving the corresponding 4-quinolone amino acid. In contrast, Boc-l-Kyn(CHO)-OMe was stable under these conditions, demonstrating that removing one of the electron withdrawing groups from the aforementioned building blocks prevents enolization in 2MP/DMF. Hence, a new synthesis of daptomycin was developed using Fmoc-l-Kyn(Boc)-OH, which is prepared in two steps from Fmoc-l-Trp(Boc)-OH, that proceeded with an unprecedented 22% overall yield. The simplicity and efficiency of this synthesis will facilitate the preparation of analogs of daptomycin. In addition, the elucidation of this side reaction will simplify preparation of other Kyn-containing natural products via Fmoc SPPS.
Collapse
Affiliation(s)
- Ryan Moreira
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, CanadaN2L 3G1.
| | | | | |
Collapse
|
12
|
Chemoenzymatic synthesis of daptomycin analogs active against daptomycin-resistant strains. Appl Microbiol Biotechnol 2020; 104:7853-7865. [PMID: 32725322 PMCID: PMC7447621 DOI: 10.1007/s00253-020-10790-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 05/21/2020] [Accepted: 07/19/2020] [Indexed: 12/18/2022]
Abstract
Abstract Daptomycin is a last resort antibiotic for the treatment of infections caused by many Gram-positive bacterial strains, including vancomycin-resistant Enterococcus (VRE) and methicillin- and vancomycin-resistant Staphylococcus aureus (MRSA and VRSA). However, the emergence of daptomycin-resistant strains of S. aureus and Enterococcus in recent years has renewed interest in synthesizing daptomycin analogs to overcome resistance mechanisms. Within this context, three aromatic prenyltransferases have been shown to accept daptomycin as a substrate, and the resulting prenylated analog was shown to be more potent against Gram-positive strains than the parent compound. Consequently, utilizing prenyltransferases to derivatize daptomycin offered an attractive alternative to traditional synthetic approaches, especially given the molecule’s structural complexity. Herein, we report exploiting the ability of prenyltransferase CdpNPT to synthesize alkyl-diversified daptomycin analogs in combination with a library of synthetic non-native alkyl-pyrophosphates. The results revealed that CdpNPT can transfer a variety of alkyl groups onto daptomycin’s tryptophan residue using the corresponding alkyl-pyrophosphates, while subsequent scaled-up reactions suggested that the enzyme can alkylate the N1, C2, C5, and C6 positions of the indole ring. In vitro antibacterial activity assays using 16 daptomycin analogs revealed that some of the analogs displayed 2–80-fold improvements in potency against MRSA, VRE, and daptomycin-resistant strains of S. aureus and Enterococcus faecalis. Thus, along with the new potent analogs, these findings have established that the regio-chemistry of alkyl substitution on the tryptophan residue can modulate daptomycin’s potency. With additional protein engineering to improve the regio-selectivity, the described method has the potential to become a powerful tool for diversifying complex indole-containing molecules. Key points • CdpNPT displays impressive donor promiscuity with daptomycin as the acceptor. • CdpNPT catalyzes N1-, C2-, C5-, and C6-alkylation on daptomycin’s tryptophan residue. • Differential alkylation of daptomycin’s tryptophan residue modulates its activity. Electronic supplementary material The online version of this article (10.1007/s00253-020-10790-x) contains supplementary material, which is available to authorized users.
Collapse
|
13
|
Chow HY, Po KHL, Jin K, Qiao G, Sun Z, Ma W, Ye X, Zhou N, Chen S, Li X. Establishing the Structure-Activity Relationship of Daptomycin. ACS Med Chem Lett 2020; 11:1442-1449. [PMID: 32676152 DOI: 10.1021/acsmedchemlett.0c00175] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 06/03/2020] [Indexed: 12/30/2022] Open
Abstract
Daptomycin is effective in treating infections caused by antibiotic-resistant Gram-positive pathogens, including methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococci (VRE), and vancomycin-resistant S. aureus (VRSA). Due to its distinct mechanism of action toward multidrug-resistant bacteria, daptomycin provides an attractive structural motif to generate new daptomycin-based antibiotics to combat the problem of bacterial resistance. In this study, we used the total synthesis method to produce daptomycin analogues with a variety in terms of types and sites of modifications. Five classes of daptomycin analogues were synthesized, and the antimicrobial activities of the analogues were analyzed by several biological assays. From this study, we established a comprehensive structure-activity relationship of daptomycin which will lay the foundation for the further development of daptomycin-based antibiotics.
Collapse
Affiliation(s)
- Hoi Yee Chow
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Kathy Hiu Laam Po
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Kang Jin
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Guanlin Qiao
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Zhenquan Sun
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Wenjie Ma
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Xiyun Ye
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Ning Zhou
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Xuechen Li
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Pok Fu Lam, Hong Kong
| |
Collapse
|
14
|
Kralt B, Moreira R, Palmer M, Taylor SD. Total Synthesis of Analogs of A54145D and A54145A 1 for Structure-Activity Relationship Studies. J Org Chem 2020; 85:2213-2219. [PMID: 31873009 DOI: 10.1021/acs.joc.9b02922] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The total solid-phase synthesis and in vitro biological activity of a series of analogs of A54145 factor D (A5D) and A54145 factor A1 (A5A1), two cyclic lipodepsipeptide antibiotics, are reported. An on-resin cyclization strategy was employed to prepare A5A1 analogs in which Thr4, the residue involved in the depsi (ester) bond, was replaced with either diaminopropionic acid (DAPA), (2S,3R)-diaminobutyric acid (DABA), or serine, effectively replacing the ring-closing ester bond with an amide linkage or with a primary ester. Antibacterial studies with these four analogs revealed that, contrary to a previous report, replacing the ester bond with an amide bond significantly reduces biological activity, and that both the ester bond and the methyl group at the γ-position of Thr4 are crucial for activity. Consistent with literature reports, we found that the single substitution of either 3-hydroxyasparagine (HOAsn) or 3-methoxyaspartate (MeOAsp) with Asn or Asp, respectively, in A5D is more detrimental to activity than the double substitution where both HOAsn and MeOAsp are replaced with Asn or Asp, respectively.
Collapse
Affiliation(s)
- Braden Kralt
- Department of Chemistry , University of Waterloo , 200 University Avenue West , Waterloo , Ontario N2L 3G1 , Canada
| | - Ryan Moreira
- Department of Chemistry , University of Waterloo , 200 University Avenue West , Waterloo , Ontario N2L 3G1 , Canada
| | - Michael Palmer
- Department of Chemistry , University of Waterloo , 200 University Avenue West , Waterloo , Ontario N2L 3G1 , Canada
| | - Scott D Taylor
- Department of Chemistry , University of Waterloo , 200 University Avenue West , Waterloo , Ontario N2L 3G1 , Canada
| |
Collapse
|
15
|
Xu B, Hermant Y, Yang S, Harris PWR, Brimble MA. A Versatile Boc Solid Phase Synthesis of Daptomycin and Analogues Using Site Specific, On‐Resin Ozonolysis to Install the Kynurenine Residue. Chemistry 2019; 25:14101-14107. [DOI: 10.1002/chem.201903725] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Buzhe Xu
- School of Chemical SciencesThe University of Auckland 23 Symonds Street Auckland 1142 New Zealand
- Maurice Wilkins Centre for Molecular BiodiscoverySchool of Biological SciencesThe University of Auckland Auckland 1142 New Zealand
| | - Yann Hermant
- School of Chemical SciencesThe University of Auckland 23 Symonds Street Auckland 1142 New Zealand
- Maurice Wilkins Centre for Molecular BiodiscoverySchool of Biological SciencesThe University of Auckland Auckland 1142 New Zealand
| | - Sung‐Hyun Yang
- School of Chemical SciencesThe University of Auckland 23 Symonds Street Auckland 1142 New Zealand
| | - Paul W. R. Harris
- School of Chemical SciencesThe University of Auckland 23 Symonds Street Auckland 1142 New Zealand
- School of Biological SciencesThe University of Auckland 3A Symonds Street Auckland 1142 New Zealand
- Maurice Wilkins Centre for Molecular BiodiscoverySchool of Biological SciencesThe University of Auckland Auckland 1142 New Zealand
| | - Margaret A. Brimble
- School of Chemical SciencesThe University of Auckland 23 Symonds Street Auckland 1142 New Zealand
- School of Biological SciencesThe University of Auckland 3A Symonds Street Auckland 1142 New Zealand
- Maurice Wilkins Centre for Molecular BiodiscoverySchool of Biological SciencesThe University of Auckland Auckland 1142 New Zealand
| |
Collapse
|
16
|
Noden M, Moreira R, Huang E, Yousef A, Palmer M, Taylor SD. Total Synthesis of Paenibacterin and Its Analogues. J Org Chem 2019; 84:5339-5347. [DOI: 10.1021/acs.joc.9b00364] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Michael Noden
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Ryan Moreira
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - En Huang
- Department of Food Science and Technology, The Ohio State University, 2015 Fyffe Court, Columbus, Ohio 43210, United States
| | - Ahmed Yousef
- Department of Food Science and Technology, The Ohio State University, 2015 Fyffe Court, Columbus, Ohio 43210, United States
| | - Michael Palmer
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Scott D. Taylor
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| |
Collapse
|
17
|
Wood TM, Martin NI. The calcium-dependent lipopeptide antibiotics: structure, mechanism, & medicinal chemistry. MEDCHEMCOMM 2019; 10:634-646. [PMID: 31191855 DOI: 10.1039/c9md00126c] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 03/20/2019] [Indexed: 12/19/2022]
Abstract
To push back the growing tide of antibacterial resistance the discovery and development of new antibiotics is a must. In recent years the calcium-dependent lipopeptide antibiotics (CDAs) have emerged as a potential source of new antibacterial agents rich in structural and mechanistic diversity. All CDAs share a common lipidated cyclic peptide motif containing amino acid side chains that specifically chelate calcium. It is only in the calcium bound state that the CDAs achieve their potent antibacterial activities. Interestingly, despite their common structural features, the mechanisms by which different CDAs target bacteria can vary dramatically. This review provides both a historic context for the CDAs while also addressing the state of the art with regards to their discovery, optimization, and antibacterial mechanisms.
Collapse
Affiliation(s)
- Thomas M Wood
- Department of Chemical Biology & Drug Discovery , Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands.,Biological Chemistry Group , Institute of Biology Leiden , Leiden University , Sylvius Laboratories , Sylviusweg 72 , 2333 BE Leiden , The Netherlands . ; Tel: +31 (0)6 1878 5274
| | - Nathaniel I Martin
- Biological Chemistry Group , Institute of Biology Leiden , Leiden University , Sylvius Laboratories , Sylviusweg 72 , 2333 BE Leiden , The Netherlands . ; Tel: +31 (0)6 1878 5274
| |
Collapse
|