Abstract
Acquired immunodeficiency syndrome (AIDS) caused by the human immunodeficiency virus (HIV) continues to be a public health problem. In 2020, 680,000 people died from HIV-related causes, and 1.5 million people were infected. Antiretrovirals are a way to control HIV infection but not to cure AIDS. As such, effective treatment must be developed to control AIDS. Developing a drug is not an easy task, and there is an enormous amount of work and economic resources invested. For this reason, it is highly convenient to employ computer-aided drug design methods, which can help generate and identify novel molecules. Using the de novo design, novel molecules can be developed using fragments as building blocks. In this work, we develop a virtual focused compound library of HIV-1 viral protease inhibitors from natural product fragments. Natural products are characterized by a large diversity of functional groups, many sp3 atoms, and chiral centers. Pseudo-natural products are a combination of natural products fragments that keep the desired structural characteristics from different natural products. An interactive version of chemical space visualization of virtual compounds focused on HIV-1 viral protease inhibitors from natural product fragments is freely available in the supplementary material.
Highlights
The acquired immunodeficiency syndrome (AIDS) caused by the human immunodeficiency virus (HIV) is a major global public health concern
As mentioned in the Introduction and Methods sections, new chemical compounds were built from two commercially available libraries: 4063 ChemDiv fragments enriched with sp3 carbons, 4160 Enamine natural products fragments, and 184,769 COlleCtion of Open NatUral producTs (COCONUT)
We developed an HIV-1 virtual focused library using de novo design based on enumerated libraries of compounds from fragment libraries
Summary
The acquired immunodeficiency syndrome (AIDS) caused by the human immunodeficiency virus (HIV) is a major global public health concern. Organization (WHO) reported that approximately 37.7 million people live with HIV out of. In 2020, 680,000 people died from HIV-related causes and 1.5 million people acquired it [1]. There is no definite treatment for AIDS. It is necessary to collaborate to develop a treatment since the antiretroviral drugs currently approved by Food and Drug Administration (FDA) to clinical use only control AIDS and prevent HIV-1 transmission between individuals (Figure 1 and Table 1) [2,3,4]. Computer-aided drug design (CADD) has contributed to yielding several drugs into the clinic, yet it has several challenges ahead [7]. Available online: http://rdkit.org (accessed on 21 May 2021)
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