Nature Inspired Small Molecules for Chemical Biology

Abstract

Chemical biology and drug discovery are instrumental sciences to address unmet medical needs and to gain a deeper understanding of normal and disease state biology in mammalian systems. Unlike most genetic tools, the small molecule modulation of biology is reversible, controllable in space, time and quantity, avoids the removal of gene products from cellular systems and thus enables perturbation of biology in its native state. Natural products, their derivatives as well as small molecules based on the core‐scaffolds of natural products including natural product fragments allow targeting unique, biologically relevant fractions of chemical space that may deliver quality tool compounds. In this essay, we discuss various synthesis approaches inspired by natural products to deliver biologically active small molecules. We argue and provide evidence that inspiration by natural product structure remains a powerful guiding principle for the development of novel approaches to the study biology by means of novel bioactive small molecules.

Natural Products as Sources of New Drugs over the Nearly Four Decades from 01/1981 to 09/2019

“…In addition to the citations given in our previous reviews, there are some recent review articles that can be consulted that demonstrate how “privileged structures from Nature” are sources of molecular skeletons around which one may build libraries. These are well described by Kumar and Waldmann, and a “hunt for an optimization of peptide macrocycles” is well described by White and Craik . In addition, the 2018 discussion by Chen et al on the chemical space occupied by natural products is also highly relevant.…”

“…Currently there are a number of other agents that are directed against the same targets as these two in current phase III clinical trials, etrasimod (47) and ponesimod (48), with another in phase II clinical trials, amiselimod (49), and one, ozanimod (50), which has been preregistered in both the USA (FDA) and the EU (EMA). To close out this section, in 2017, Dyckman published an excellent perspective in the Journal of Medicinal Chemistry that gave a thorough background on these agents and their derivation, which is well worth consulting.…”

Chemical Evolution of Natural Product Structure

“…The importance of small molecules that can perturb biological systems in a controlled fashion is underpinned by their successful applications in chemical biology 1 and medicine. 2 Nevertheless, the continued exploration of biologically relevant chemical space for the discovery of new small molecules remains an essential task for the better understanding of biological processes and for the advancement of therapeutics.…”

The PIFA-initiated oxidative cyclization of 2-(3-butenyl)quinazolin-4(3H)-ones – an efficient approach to 1-(hydroxymethyl)-2,3-dihydropyrrolo[1,2-a]quinazolin-5(1H)-ones

“…Since the application of the obtained compounds in early drug discovery is anticipated, it is important to assess their suitability for the synthesis of compound libraries relevant to medicinal chemistry. While many chemoinformatic tools are available for that purpose, we have turned our attention to Ertl's natural product likeness (NPL) score since the target compounds were designed as natural product analogs [1][2][3][4]. In its essence, the NPL score for any molecule estimates its similarity to natural products vs synthetic molecules; it is based on the occurrence frequencies of the corresponding molecular fragments in the two series mentioned above.…”

“…An important design concept in current drug discovery includes structural modifications of naturally occurring compounds to provide novel, sp 3 -enriched scaffolds with increased propensity to generate potent lead structures with favorable physicochemical properties [1][2][3][4]. In light of this, synthesis of compounds that are close analogs of natural compounds is an important task for the synthetic organic chemistry, and this approach has already provided successful results in the view of reaching biological activity.…”