<?xml version="1.0" encoding="us-ascii"?>
<!-- DFIN ActiveDisclosure(SM) XBRL Schema Document - http://www.dfinsolutions.com/ -->
<!-- Creation Date      : 2021-11-15T20:02:09.8114324+00:00 -->
<!-- Version            : 5.0.1.702 -->
<!-- Package ID         : b2e2de50f5764156add010462076a9ad -->
<!-- Copyright (c) 2021 Donnelley Financial Solutions, Inc. All Rights Reserved. -->
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  <xsd:element id="sndx_StockIssuedDuringPeriodValuePreFundedWarrantExchange" name="StockIssuedDuringPeriodValuePreFundedWarrantExchange" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="sndx_StockIssuedDuringPeriodSharesExerciseOfWarrants" name="StockIssuedDuringPeriodSharesExerciseOfWarrants" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="sndx_StockIssuedDuringPeriodValueDirectOffering" name="StockIssuedDuringPeriodValueDirectOffering" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="sndx_StockIssuedDuringPeriodValuePreFundedCommonStockWarrantsFromDirectOffering" name="StockIssuedDuringPeriodValuePreFundedCommonStockWarrantsFromDirectOffering" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="sndx_StockIssuedDuringPeriodValueCommonStockWarrantWithDirectOffering" name="StockIssuedDuringPeriodValueCommonStockWarrantWithDirectOffering" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="sndx_AdjustmentsToAdditionalPaidInCapitalDeemedDividendFromRepricingWarrants" name="AdjustmentsToAdditionalPaidInCapitalDeemedDividendFromRepricingWarrants" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="sndx_AdjustmentsToAdditionalPaidInCapitalRepricingWarrants" name="AdjustmentsToAdditionalPaidInCapitalRepricingWarrants" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="sndx_SeriesOneAndTwoMember" name="SeriesOneAndTwoMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="sndx_StockIssuedDuringPeriodSharesPreFundedWarrantExchange" name="StockIssuedDuringPeriodSharesPreFundedWarrantExchange" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="sndx_StockIssuedDuringPeriodSharesDirectOffering" name="StockIssuedDuringPeriodSharesDirectOffering" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="sndx_StockIssuedDuringPeriodValueOfferingExpenses" name="StockIssuedDuringPeriodValueOfferingExpenses" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="sndx_StockIssuedDuringPeriodValuePreFundedCommonStockWarrantOfferingExpenses" name="StockIssuedDuringPeriodValuePreFundedCommonStockWarrantOfferingExpenses" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="sndx_StockIssuedDuringPeriodValueAtTheMarketOfferingExpenses" name="StockIssuedDuringPeriodValueAtTheMarketOfferingExpenses" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="sndx_CowenAndCompanyLLCMember" name="CowenAndCompanyLLCMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="sndx_AtTheMarketEquityOfferingSalesAgreementMember" name="AtTheMarketEquityOfferingSalesAgreementMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="sndx_SeriesWarrantsMember" name="SeriesWarrantsMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="sndx_SeriesOneWarrantsMember" name="SeriesOneWarrantsMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="sndx_SeriesTwoWarrantsMember" name="SeriesTwoWarrantsMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="sndx_NumberOfSeriesOfWarrants" name="NumberOfSeriesOfWarrants" type="xbrli:integerItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="sndx_ClassOfWarrantOrRightTerm" name="ClassOfWarrantOrRightTerm" type="xbrli:durationItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="sndx_OfferingPricePerShare" name="OfferingPricePerShare" type="dtr-types:perShareItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="sndx_GrossProceedsFromOffering" name="GrossProceedsFromOffering" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="sndx_OfferingCost" name="OfferingCost" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="sndx_WarrantsExercisedPeriod" name="WarrantsExercisedPeriod" type="xbrli:gYearItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="sndx_MaximumPeriodAllowedToIncreaseBeneficialOwnershipLimitationAfterNotice" name="MaximumPeriodAllowedToIncreaseBeneficialOwnershipLimitationAfterNotice" type="xbrli:durationItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="sndx_ExerciseOfWarrantsLowerLimitAfterExerciseAsPercentageOfCommonStock" name="ExerciseOfWarrantsLowerLimitAfterExerciseAsPercentageOfCommonStock" type="dtr-types:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="sndx_MaximumBeneficialOwnershipLimitationPercentage" name="MaximumBeneficialOwnershipLimitationPercentage" type="dtr-types:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="sndx_FairValueOfWarrants" name="FairValueOfWarrants" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit" />
</xsd:schema>
