Atomistic Simulations and Design in Biology

Mechanisms underlying biology at a molecular level are explored through identifying and/or mapping the interactions of proteins with other proteins, nucleic acids, ligands. The methods/tools used are computational and combine representations at various levels, from the coarse-grained to the fully atomistic. The work builds upon foundations that are rooted in rigorous physical principles and computational biochemistry benchmarked extensively against available experimental data. Simulations complement extensive collaborations with experimental laboratories to provide incisive insights into biology at an atomic level. The group’s current research focuses on several bimolecular mechanisms including those associated with the p53 pathway, kinases, translation initiation, antimicrobials and basic computational biophysical chemistry. The molecular underpinnings of biomolecular regulation with ligand/drug discovery and protein/peptide design are translated into  (bio)technological, therapeutic and clinical settings. The toolbox used consists of: construction of models based on "imagination with a whiff of hand-waving", homology modelling, molecular dynamics, free energy landscapes, reaction paths, ligand-protein/protein-protein dockings including virtual screening, molecular design, machine learning/AI.

PEPTIDES: p53, EIF4E, KRAS & OTHER PATHWAYS

An extensive program with the p53 laboratory of Prof Sir David Lane combining computer modeling, biophysics, crystallography, molecular/cell biology, investigating the relationship between structural-functional aspects of the p53 family has revealed interesting nuances about the p53, eIF4E and KRAS pathways. These have guided us in designing a set of novel constrained (stapled/stitched) peptides (Mol Sys Des Engg 7 996 2022; J Coll Interf Sci 604 670 2021) whose ability to enter cells and specifically target the p53-MDM2 axis with nanomolar affinities, thus activating p53, has opened a new avenue for designing therapeutics (Nature Med 2013 19 120). A major effort with pharma companies focused on understanding the mechanism of cellular permeabilization (J Chem Phys 2022 156 065101; Chem Sci 2022 13 1957) and nuclear entry of these peptides and subsequently in using these peptides as probes, therapeutics, or vehicles for delivering cargo into cells (RSC Chem Biol 2022 3 916; US Patent App 11319344 2022). This is being extended to developing constrained/peptides against other targets such as KRAS (Chem Sci 2021 12 15975; US Patent App 17783224 2022), eIF4E to inhibit translation initiation for a range of cancers (Nat Commun 2022). A novel d-amino acid containing stitched peptide has been designed and validated to activate p53 and has recently been patented jointly with a pharma (US Patent App 17618751 2022). This collaboration has brought in partners from local organizations, international universities, and pharma industry. The developments and the excitement generated in the p53 field have been outlined in articles in Nature Reviews Drug Discovery, Nature Reviews in Cancer, Nature Reviews in Clinical Oncology, published by the joint efforts of teams from Singapore, Karolinska, Cambridge & Harvard Universities. The program has been supported by generous funding from A*STAR and pharma.

Novel Antimicrobials

A highly successful interdisciplinary program with the group of late Prof Beuerman at the Singapore Eye Research Institute and researchers at National University of Singapore, Singapore General Hospital, Duke-NUS and Tan Tok Sing Hospital has resulted in the design of several novel antimicrobials. These molecules target bacterial membranes rapidly, are non-toxic to human cells and appear to avert resistance in bacteria (Front Pharmacol 2793 2021). The molecules work against a range of gram-positive and gram-negative organisms (Biomaterials 122004 2023) including resistant MRSA. A combination of a small molecule LC100 (designed using out in-membrane fragment-based design platform (BBA Biomembranes 1848 1023 2015; WO2014039015 A1) and peptide (Colistin) has been developed that appears to be extremely potent at killing resistant Gram negatives (US Patent App 17612013 2022). This program is of critical importance as the spread of antimicrobial resistance is an impending global epidemic.

Figure 3. Combining outer-membrane permeabilizer (Colistin) with inner membrane disrupting small molecule

Figure 4. Combination results in 1.2 log reduction (mice thigh infection)

Translation

The virtual screening, design and simulation efforts of the group are extended to collaborations with various groups within A*STAR (including the Experimental Drug Discovery Centre, IMCB, IMB, SIGN, p53Lab, MEL, SBIC, ICES), the hospitals in Singapore, research centers (National Cancer Centre, Cancer Science Institute, LKC), universities (NUS, NTU, Duke-NUS) and organizations elsewhere (Univ of Cambridge, Karolinska Instt, MSKCC, Johns Hopkins Univ, val d’Hebron, Univ Miami), who carry out the experimental investigations of the compounds. The projects cover a diverse landscape and include bladder cancer (Mol Can Res 20 1516 2022), breast cancer (Nat Commun 13 5258 2022), NSCLC (Cancer Disc 11 126 2021) supported by more fundamental studies such as the role of phosphorylation (Proteins 90 2009 2022; Elife 10 e68678 2021). Programs that combine the strengths of various institutes, hospitals and universities in Singapore towards peptide engineering for bioimaging agents (CITI program), precision medicine (national platform PRECISE), therapeutics discovery (STDR programs) generously funded by grants such as the Industry Alignment Fund Pre-Positioning grants, NMRC etc. As part of the National Precision Medicine program (PRECISE), in a large island wide effort, this project of national significance is dedicated to developing and mining platform for predicting the effects of missense variations in proteins and their effects on drugs as an aid to assist clinicians (Nature Genetics 55 178 2023; Cell 179 736 2019). This program gains further strategic significance with the demonstration of the power of modelling methods to work in complement with experimentalists to influence clinical decisions (Nat Commun 11 1556 2020; Cancer Discovery 11 126 2021). Currently the program is focused on scaling such applications to large scale interrogations of the effects of SNPs/mutations.

The success of the group in interfacing the nanoscale with experimental observations has encouraged several experimental groups to participate with us. These have also resulted in joint graduate programs with various universities including Southampton, Manchester, Essex. New programs including the interface of AI and/or quantum computing in drug discovery are being launched.

• Verma & Lane Covalent Rescue of mutant p53. Cancer Discovery 13 14 (2023)
• Wong et al The Singapore national precision medicine strategy. Nature Genetics 55 178 (2023)
• Palafox et al High p16 expression and heterozygous RB1 loss are biomarkers for CDK4/6 inhibitor resistance in ER+ breast cancer Nature Commun 13 5258 (2022)
• Frosi et al Engineering an autonomous VH domain to modulate intracellular pathways and to interrogate the eIF4F complex Nature Commun 13 4854 (2022)
• Cocco et al TRK xDFG mutations trigger a sensitivity switch from type I to II kinase inhibitors. Cancer Discovery 11 126 (2021)
• Arruabarrena-Aristorena et al FOXA1 mutations reveal distinct chromatin profiles and influence therapeutic response in breast cancer. Cancer Cell 38 534 (2020)
• Khoo et al Drugging the p53pathway: understanding the route toclinical efficiency. Nat Rev Drug Discov 13 217 (2014).
• Goudie et al Multiple self-healing squamous epthelioma is caused by a disease-specific spectrum of mutations in TGBR1. Nature Genetics 43 365 (2011).
• Cheok et al Translating p53 into the clinic. Nat Rev Clin Oncol 8 25 (2011).
• Brown et al Awakening guardian angels: drugging the p53 pathway. Nature Reviews Cancer 9 862 (2009)