Revision of the Peniroquesine Biosynthetic Pathway by Retro-Biosynthetic Theoretical Analysis: Ring Strain Controls the Unique Carbocation Rearrangement Cascade

DFT Study on Retigerane-Type Sesterterpenoid Biosynthesis: Initial Conformation of GFPP Regulates Biosynthetic Pathway, Ring-Construction Order and Stereochemistry

Retigerane-type sesterterpenoids, which feature a unique 5/6/5/5/5 fused pentacyclic structure with an angular-type triquinane moiety, are biosynthesized via successive carbocation-mediated reactions triggered by terpene cyclases. However, the precise biosynthetic pathways/mechanisms, wherein steric inversion of the carbon skeleton occurs at least once, remain elusive. Two plausible reaction pathways have been proposed, which differ in the order of ring cyclization: A → B/C → D/E-ring(s) (Route 1) and A → E → B → C/D-ring(s) (Route 2). Since the reaction intermediates of these complicated domino-type reaction sequences are experimentally inaccessible, we employed comprehensive density functional theory (DFT) calculations to evaluate these routes. The results indicate that retigeranin biosynthesis proceeds via Route 2 involving a multistep carbocation cascade, in which the order of ring cyclization (A → E → B → C/D) is the key to constructing the angular 5/5/5 triquinane structure with the correct stereochemistry at C3. The result also suggests that slight differences in the initial conformation have a significant effect on the order of cyclization and steric inversion. The computed pathway/mechanism also provides a rational basis for the formation of various related terpenes/terpenoids.

Naturally Occurring Norsteroids and Their Design and Pharmaceutical Application

The main focus of this review is to introduce readers to the fascinating class of lipid molecules known as norsteroids, exploring their distribution across various biotopes and their biological activities. The review provides an in-depth analysis of various modified steroids, including A, B, C, and D-norsteroids, each characterized by distinct structural alterations. These modifications, which range from the removal of specific methyl groups to changes in the steroid core, result in unique molecular architectures that significantly impact their biological activity and therapeutic potential. The discussion on A, B, C, and D-norsteroids sheds light on their unique configurations and how these structural modifications influence their pharmacological properties. The review also presents examples from natural sources that produce a diverse array of steroids with distinct structures, including the aforementioned A, B, C, and D-nor variants. These compounds are sourced from marine organisms like sponges, soft corals, and starfish, as well as terrestrial entities such as plants, fungi, and bacteria. The exploration of these steroids encompasses their biosynthesis, ecological significance, and potential medical applications, highlighting a crucial area of interest in pharmacology and natural product chemistry. The review emphasizes the importance of researching these steroids for drug development, particularly in addressing diseases where conventional medications are inadequate or for conditions lacking sufficient therapeutic options. Examples of norsteroid synthesis are provided to illustrate the practical applications of this research.

QM/MM Study of the Catalytic Mechanism and Substrate Specificity of the Aromatic Substrate C-Methyltransferase Fur6

In the field of medical chemistry and other organic chemistry, introducing a methyl group into a designed position has been difficult to achieve. However, owing to the vigorous developments in the field of enzymology, methyltransferases are considered potential tools for addressing this problem. Within the methyltransferase family, Fur6 catalyzes the methylation of C3 of 1,2,4,5,7-pentahydroxynaphthalene (PHN) using S-adenosyl-l-methionine (SAM) as the methyl donor. Here, we report the catalytic mechanism and substrate specificity of Fur6 based on computational studies. Our molecular dynamics (MD) simulation studies reveal the reactive form of PHN and its interactions with the enzyme. Our hybrid quantum mechanics/molecular mechanics (QM/MM) calculations suggest the reaction pathway of the methyl transfer step in which the energy barrier is 8.6 kcal mol-1. Our free-energy calculations with a polarizable continuum model (PCM) indicate that the final deprotonation step of the methylated intermediate occurs after it is ejected into the water solvent from the active center pocket of Fur6. Additionally, our studies on the protonation states, the highest occupied molecular orbital (HOMOs), and the energy barriers of the methylation reaction for the analogs of PHN demonstrate the mechanism of the specificity to PHN. Our study provides valuable insights into Fur6 chemistry, contributing to a deeper understanding of molecular mechanisms and offering an opportunity to engineer the enzyme to achieve high yields of the desired product(s).

Theoretical Study of Natural Product Biosynthesis Using Computational Chemistry

The biosynthetic pathways of natural products are complicated, and it is difficult to fully elucidate their details using experimental chemistry alone. In recent years, efforts have been made to elucidate the biosynthetic reaction mechanisms by combining computational and experimental methods. In this review, we will discuss the biosynthetic studies using computational chemistry for various terpene compounds such as cyclooctatin, sesterfisherol, quiannulatene, trichobrasilenol, asperterpenol, preasperterpenoid, spiroviolene, and mangicol.

Unraveling the role of prenyl side-chain interactions in stabilizing the secondary carbocation in the biosynthesis of variexenol B

Terpene cyclization reactions involve a number of carbocation intermediates. In some cases, these carbocations are stabilized by through-space interactions with π orbitals. Several terpene/terpenoids, such as sativene, santalene, bergamotene, ophiobolin and mangicol, possess prenyl side chains that do not participate in the cyclization reaction. The role of these prenyl side chains has been partially investigated, but remains elusive in the cyclization cascade. In this study, we focus on variexenol B that is synthesized from iso-GGPP, as recently reported by Dickschat and co-workers, and investigate the possibility of through-space interactions with prenyl side chains using DFT calculations. Our calculations show that (i) the unstable secondary carbocation is stabilized by the cation-π interaction from prenyl side chains, thereby lowering the activation energy, (ii) the four-membered ring formation is completed through bridging from the exomethylene group, and (iii) the annulation from the exomethylene group proceeds in a barrier-free manner.

Mechanistic Investigation of the Degradation Pathways of α-β/α-α Bridged Epipolythiodioxopiperazines (ETPs)

Epipolythiodioxopiperazines (ETPs) make up a class of biologically active fungal metabolites with a transannular disulfide bridge. In this work, we used DFT calculations to examine in detail the degradation (desulfurization) pathways of α-β/α-α bridged ETPs. The chemical stability of ETPs is influenced by the type of sulfur bridge, the structural features, and the storage conditions. Our results suggest appropriate protection of the phenolic OH of ETPs would improve various pharmaceutically relevant properties, including bioavailability.