Phyo Phyo Zin - SandboxAQ | LinkedIn (2025)

Issued May 2020

See credential

Issued Jan 2015

Imatinib, a 2-phenylaminopyridine-based BCR-ABL tyrosine kinase inhibitor, is a highly effective drug for treating Chronic Myeloid Leukemia (CML). However, cases of drug resistance are constantly emerging due to various mutations in the ABL kinase domain; thus, it is crucial to identify novel bioactive analogues. Reliable QSAR models and molecular docking protocols have been shown to facilitate the discovery of new compounds from chemical libraries prior to experimental testing. However, as the…

Imatinib, a 2-phenylaminopyridine-based BCR-ABL tyrosine kinase inhibitor, is a highly effective drug for treating Chronic Myeloid Leukemia (CML). However, cases of drug resistance are constantly emerging due to various mutations in the ABL kinase domain; thus, it is crucial to identify novel bioactive analogues. Reliable QSAR models and molecular docking protocols have been shown to facilitate the discovery of new compounds from chemical libraries prior to experimental testing. However, as the vast majority of QSAR models strictly relies on 2D descriptors, the rise of 3D descriptors directly computed from molecular dynamics simulations offers new opportunities to potentially augment the reliability of QSAR models. Herein, we employed molecular docking and molecular dynamics on a large series of Imatinib derivatives and developed an ensemble of QSAR models relying on deep neural nets (DNN) and hybrid sets of 2D/3D/MD descriptors in order to predict the binding affinity and inhibition potencies of those compounds. Through rigorous validation tests, we showed that our DNN regression models achieved excellent external prediction performances for the pKi data set (n = 555, R2 ≥ 0.71. and MAE ≤ 0.85), and the pIC50 data set (n = 306, R2 ≥ 0.54. and MAE ≤ 0.71) with strict validation protocols based on external test sets and 10-fold native and nested cross validations. Interestingly, the best DNN and random forest models performed similarly across all descriptor sets. In fact, for this particular series of compounds, our external test results suggest that incorporating additional 3D protein–ligand binding site fingerprint, descriptors, or even MD time-series descriptors did not significantly improve the overall R2 but lowered the MAE of DNN QSAR models. Those augmented models could still help in identifying and understanding the key dynamic protein–ligand interactions to be optimized for further molecular design.

Macrolactones, macrocyclic lactones with at least twelve atoms within the core ring, include diverse natural products such as macrolides with potent bioactivities (e.g. antibiotics) and useful drug-like characteristics. We have developed MacrolactoneDB, which integrates nearly 14,000 existing macrolactones and their bioactivity information from different public databases, and new molecular descriptors to better characterize macrolide structures. The chemical distribution of MacrolactoneDB was…

Macrolactones, macrocyclic lactones with at least twelve atoms within the core ring, include diverse natural products such as macrolides with potent bioactivities (e.g. antibiotics) and useful drug-like characteristics. We have developed MacrolactoneDB, which integrates nearly 14,000 existing macrolactones and their bioactivity information from different public databases, and new molecular descriptors to better characterize macrolide structures. The chemical distribution of MacrolactoneDB was analyzed in terms of important molecular properties and we have utilized three targets of interest (Plasmodium falciparum, Hepatitis C virus and T-cells) to demonstrate the value of compiling this data. Regression machine learning models were generated to predict biological endpoints using seven molecular descriptor sets and eight machine learning algorithms. Our results show that merging descriptors yields the best predictive power with Random Forest models, often boosted by consensus or hybrid modeling approaches. Our study provides cheminformatics insights into this privileged, underexplored structural class of compounds with high therapeutic potential.

We report on a new cheminformatics enumeration technology—SIME, synthetic insight-based macrolide enumerator—a new and improved software technology. SIME can enumerate fully assembled macrolides with synthetic feasibility by utilizing the constitutional and structural knowledge extracted from biosynthetic aspects of macrolides. Taken into account by the software are key information such as positions in macrolide structures at which chemical components can be inserted, and the types of…

We report on a new cheminformatics enumeration technology—SIME, synthetic insight-based macrolide enumerator—a new and improved software technology. SIME can enumerate fully assembled macrolides with synthetic feasibility by utilizing the constitutional and structural knowledge extracted from biosynthetic aspects of macrolides. Taken into account by the software are key information such as positions in macrolide structures at which chemical components can be inserted, and the types of structural motifs and sugars of interest that can be synthesized and incorporated at those positions. Additionally, we report on the chemical distribution analysis of the newly SIME-generated V1B (virtual 1 billion) library of macrolides. Those compounds were built based on the core of the Erythromycin structure, 13 structural motifs and a library of sugars derived from eighteen bioactive macrolides. This new enumeration technology can be coupled with cheminformatics approaches such as QSAR modeling and molecular docking to aid in drug discovery for rational designing of next generation macrolide therapeutics with desirable pharmacokinetic properties.

We report on the development of a cheminformatics enumeration technology and the analysis of a resulting large dataset of virtual macrolide scaffolds. Although macrolides have been shown to have valuable biological properties, there is no ready-to-screen virtual library of diverse macrolides in the public domain. Conducting molecular modeling (especially virtual screening) of these complex molecules is highly relevant as the organic synthesis of these compounds, when feasible, typically…

We report on the development of a cheminformatics enumeration technology and the analysis of a resulting large dataset of virtual macrolide scaffolds. Although macrolides have been shown to have valuable biological properties, there is no ready-to-screen virtual library of diverse macrolides in the public domain. Conducting molecular modeling (especially virtual screening) of these complex molecules is highly relevant as the organic synthesis of these compounds, when feasible, typically requires many synthetic steps, and thus dramatically slows the discovery of new bioactive macrolides. Herein, we introduce a cheminformatics approach and associated software that allows for designing and generating libraries of virtual macrocycle/macrolide scaffolds with user-defined constitutional and structural constraints. To study the chemical diversity of such generated molecules, we enumerated V1M (Virtual 1 million Macrolide scaffolds) library, each containing twelve common structural motifs. For each macrolide scaffold, we calculated several key properties, such as molecular weight, hydrogen bond donors/acceptors, topological polar surface area. In this study, we discuss (1) the initial concept and current features of our PKS (polyketides) Enumerator software, (2) the chemical diversity and distribution of structural motifs in V1M library, and (3) the unique opportunities for future virtual screening of such enumerated ensembles of macrolides. Importantly, V1M is provided in the Supplementary Material of this paper allowing other researchers to conduct any type of molecular modeling and virtual screening studies. Therefore, this technology for enumerating extremely large libraries of macrolide scaffolds could hold a unique potential in the field of computational chemistry and drug discovery for rational designing of new antibiotics and anti-cancer agents.

We documented the experiences of some international students at Berea College, KY, USA. The students discuss four major topics which are:
1. Culture shock experiences,
2. Experiences with roommates and host families
3. Things they would like to take away from US to their countries, and
4. Things they would bring from their countries to US

The purpose of this project was to get required data and information to present to the government and the architectural organizations so that they can work together to preserve some historical heritage of Myanmar. I participated as an architectural intern of Design 2000 architectural firm. I worked with six Burmese architects and an English architect from England. I translated English and Burmese for the group members, photographed and sketched the old Colonial buildings in the downtown areas…

The purpose of this project was to get required data and information to present to the government and the architectural organizations so that they can work together to preserve some historical heritage of Myanmar. I participated as an architectural intern of Design 2000 architectural firm. I worked with six Burmese architects and an English architect from England. I translated English and Burmese for the group members, photographed and sketched the old Colonial buildings in the downtown areas of Yangon, and helped in the preparation of documents and presentations.

The project was monitored by Myittar Phaung Non-Profit Organization in rural areas around Yangon. There were no hospitals nearby and the transportation was difficult. Poverty was the cause of underdeveloped education, transportation, health and social awareness. The goal of the project was to inform the people of healthy living styles and to give medical treatment to those needed. I participated as a medical assistant and supervisor of the medical supplies.

A recipient of the prestigious and highly competitive AAUW 2019-2020 fellowship ($20,000) which supports exclusively for educational programs that directly benefit women and girls.

Developed ChemX in the 24-hour period of hacking while working solo without any teammates. The ChemX program takes a chemical compound and generates analogs of that target compound. It does so by fragmenting the compound into synthetically accessible building blocks and replacing each with other building blocks with similar chemical properties. Essentially, it generates a virtual chemical library by assembling chemically similar fragments and generating analogs of the target compound.

In a 24-hacking period, we developed a software, RecipeGenie which suggests dishes or cuisines along with the recipes based on the ingredients you have in your pantry. The program takes as input the photos of your pantry, executes an algorithm to find objects in those photos (i.e., the individual items), and applies a neural net to classify the objects into appropriate ingredients. Based on these individual items, it then suggests the dishes that you can make, and also suggest some recipes you…

Carlos Andres Berejnoi Bejarano and I participated in the creative storytelling at ETHDenver event and won the prize of $625.

Excerpt from chemistry graduate campus email
"Phyo Phyo Kyaw Zin (Chemistry) presented her most recent work on the development of the PKS enumerator, a software to generate large libraries of macrocycles with user-defined constrains (she showcased a dataset of 10 million compounds). This work is done in close collaboration with Dr. Gavin Williams (Chemistry, NCSU) and has applications for the virtual screening of new bioactive macrolides for the development of new antimicrobials and…

Excerpt from chemistry graduate campus email
"Phyo Phyo Kyaw Zin (Chemistry) presented her most recent work on the development of the PKS enumerator, a software to generate large libraries of macrocycles with user-defined constrains (she showcased a dataset of 10 million compounds). This work is done in close collaboration with Dr. Gavin Williams (Chemistry, NCSU) and has applications for the virtual screening of new bioactive macrolides for the development of new antimicrobials and agrochemicals."

Awarded $2000 scholarship towards my graduate studies (Ph.D) at NCSU

Along with monetary award of $250

Awarded $2000 scholarship towards my graduate studies (Ph.D) at NCSU

I was awarded second prize, along with $300, in poster presentation for my work with Dashboard Management System (DMS) at TRIWiC 2016 Conference.

August 2012 - Current

It is a non-profit organization initiated by peer volunteers from Tharapar Library and distributing health care, education and knowledge in the very poor rural areas of Yangon. I volunteered as a teacher for a monastic elementary school monitored by the monks and a few local teachers. I taught English, Mathematics and General Science to elementary level students from a variety of ages in a monastic school. This was a very challenging and rewarding experience because I encountered some students…

It is a non-profit organization initiated by peer volunteers from Tharapar Library and distributing health care, education and knowledge in the very poor rural areas of Yangon. I volunteered as a teacher for a monastic elementary school monitored by the monks and a few local teachers. I taught English, Mathematics and General Science to elementary level students from a variety of ages in a monastic school. This was a very challenging and rewarding experience because I encountered some students who were psychologically damaged because of their physically and morally corrupted society.